The Day of the Doctor of Evolution: CoE #66

TardisI was eight years old in late November 1963. I didn’t pay much attention to the TV news – some guy had been shot or something, and I wasn’t to know that C. S. Lewis had died until much later – but I was instantly taken by the eerie sound of the opening music of a new show. Yes, it was the very first episode of Dr Who, in glorious monochrome! I was a Whovian from the beginning, before it was cool. I’m so hip…

Doctor Who was all about time and space, as the famous TARDIS evidenced in its very acronym. And time and space are the very subject matter of evolution and related subjects. So in honour of the twelve (thirteen? 57?) doctors, welcome to the day of the Doctor of Evolution! [all rights reserved, patent pending]

If you open the door to evolution, you find that it is bigger inside the theory than outside. This causes some confusion to novices. Even, sometimes, for putative experts:

Judge Starling reminds Card Carrying #ENCODE members that junk DNA is not a synonym for noncoding DNA. The good Judge (a friend of the good Doctor?) also notes that junk DNA is not there to “protect” used DNA either – A Pre-Refuted Hypothesis on the Subject of “Junk DNA”.

Evolution can achieve weird and wonderful things, some of them as weird as any alien the Doctor has ever encountered. How about ant images on the wings of a fly? Pictures in my head: What is that on the wing of the fly? What does it tell us about adaptation?

Humans appear in evolution, but contrary to some (nameless) science fiction shows, they aren’t the inevitable outcome of it. Still, we are humans (some of us, anyway – hands up those with more than one heart), so we are fascinated by how we evolved and what it means.

Carl Zimmer notes that viruses have had a real role in our evolution: How Our Minds Went Viral posted at The Loom. He notes that we carry many stretches of DNA that were inserted by endogenous retroviruses (that’s the sort of technobabble you’d expect to find in a Doctor Who script) and discusses one such example.

In Catching Fire. The other oneGreg Laden considers the hypothesis that the use of fire explains much human specialities and adaptations. It’s the need of brains to eat, as it were. Mind, that means that a Time Lord must eat so much more than we do…

We evolve in other ways too. Jason Collins at Evolving Economics notes that we evolve culturally even in economics: Natural selection and saving.

And Markeyus argues that Why I,Robot should never become a reality posted at Live2Conquer (because they will evolve in ways we don’t want them to). A little dystopian, but probably not enough. On this theme, Chris Adami gives an excellent overview of something that should be a Doctor Who script: evolving machines, in Darwin inside the machine: A brief history of digital life posted at Spherical Harmonics.

David Morrison, a parasitologist (not a parasite, no!) sent us two contributions of his: the one where he claims that the history of language is not really the same as evolutionary biology – Language history and language weirdness; and another where he points out the evolutionary consequences of failing to maintain within-individual genetic diversity – Toulouse-Lautrec: family trees and networks. I wonder if the second one is a little short?

It’s not all about humans, though. While you could possibly have seen extinct organisms in life if you had a TARDIS, the rest of us have to rely on fossils. Ed Yong The Oldest Big Cat, From the Roof of the World. Meanwhile, Noah Reid at Nothing in Biology Makes Sense! explores a 52 million year old fossil sheds light on swift and hummingbird flight evolution; they even know what colour its plumage was. MSU graduate student Patric Vaelli describes research on tetrodotoxic animals (I’d never seen the word before either) in Poisons and Microbes posted at BEACON, the lab blog of a centre for evolution.

Evolution is not just a process, but it is also a theory (or rather, a set of theories and models), and like any scientific theory it requires techniques to uncover what is happening and explain it. So, no “timey-wimey” sort of explanations here, no. It’s all adult reading material (the War Doctor would understand).

Charles Goodnight explains the statistics of selection on correlated quantitative traits in Measuring Selection on Multiple Traits at Evolution in Structured Populations. Math warning (but it doesn’t look too complex). Then there’s the question whether Baker’s Yeast is a Good Model for the Evolution of Multicellularity? by Larry Moran at Sandwalk. The theme is continued in a review of a couple of recent papers:  Evolution, Variation, Development, and Strains of Artificial Life in the Reading Queue posted at Synthetic Daisies, and in Evolving multicellularity in the lab: exercises by Ford Denison. It’s relatively easy to evolve multicellularity in yeast, in the lab. Why did it take so long then in nature? Possibly, predation….

And what about time and space? One space associated with evolution is the fitness landscape, very well explained here: Smooth and rugged fitness landscapes posted at Pleiotropy.

Some bibs and bobs: Apparently, Scientists have created Detailed Map of the Dinosaur Brain according to Mike at the Everything Dinosaur Blog.

Ben Haller Timothy Farkas discusses the Ecological effects of camouflage evolution in the stick insect Timema cristinae at EcoEvoEvoEco. Apparently it adapts to novel host plants (who knew? Well, we might have expected it).

Glenn Branch considers an argument from falsifiability made by Intelligent Designist Michael Behe in Falsifia-behe-lity | NCSE posted at SLA (Science League of America; they have cool constumes and everything, but that’s the wrong genre here).

If I may be imodest, I note a few items I have posted myself in the last little while. In one – Articles of faith: The theological and philosophical origins of the concept of species – I try to argue that the notion there is a species rank is due to the efforts of 16th century theologians to fit all the “kinds” onto the Ark (it was also posted at The Conversation, a really nice site for generally intellectual popular articles). I follow it up with Yet Another Article on Species Concepts (YAAOSC, as it is increasingly known in the trade) – Are species theoretical objects? Are you bored with species concepts yet? Wait. I’m a (not the) Doctor, and I can say a lot more…

In another I roughly trace the origins of the phrase, and to an extent the concept, of “intelligent design” – The origin of “intelligent design” in the 18th and 19th centuries. If I only had a TARDIS I could have gone much farther back…

The January host will be The Genealogical World of Phylogenetic Networks.

So, there you have it. The only thing left is to state, categorically and without fear of contradiction, that the very best Doctor is Matt Smith, who acts the rest into a small blue box…

22 Comments

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22 Responses to The Day of the Doctor of Evolution: CoE #66

  1. bwana

    Lots of good reading references! Thanks

  2. I saw this post this morning and meant to make a comment. However, Larry Moran posted on it this evening. Here is the comment I left at Sandwalk:

    “I read John’s post this morning, but silly me, I didn’t realize it was a Carnival of Evolution post. I kept looking at the “CoE” and thinking “Church of England.” Serious fail on my part.

    However, my favourite sentences in John’s post are

    “If you open the door to evolution, you find that it is bigger inside the theory than outside. This causes some confusion to novices. Even, sometimes, for putative experts.”

    I’m not even a novice; I’m a postulant.”

  3. David Morrison

    John, I think that you may have misunderstood. Being Dr Who is not about acting. There is apparently more to it than that.

  4. gil

    i study biology and i think i have very strong evidence for design in nature

    a) we know that a self replicate robot that made from dna need a designer

    b) from a material prespective the ape is a self replicate robot

    a+b= the ape need a designer

    or even a self replicat watch.the evolutionist always says that a watch need a designer because it cant self rplicat. so if we will find a self replicat watch we need to say that is made by itself

    scientist even find a motor in bacteria called bacterial flagellum:

    http://www.youtube.com/watch?v=k-j5kKSk_6U

    plus: if a self replicate car cant evolve into an airplan, how can a bacteria can evolve into human ?

    the evolution say that small steps for milions years become a big steps. but according to this a lots of small steps in self replicat car (with dna) will evolve into a airplan.

    but there is no step wise from car to airplan

    evolution say that common similarity is evidence for common descent. but according to this 2 similar self replicat car are evolve from each other

    check this site

    http://creation.com/

    • bwana

      And why can’t a “self replicate car” (dinosaur) evolve into an airplane (bird)? Mutations in the car’s “DNA” could very well cause it to evolve into an airplane if environmental pressures gave its offspring a better chance of survival as an airplane. Good to see you just proved the case for evolution! Thanks for that…

    • Hey “gil”. I have an idea for you. How about you start working on spelling and grammar, and then move on to learning about basic science (math, physics, biology, etc), and then after some years delve into evolutionary biology? I know, I know, it seems like that takes quite a while, but this is what all the hundreds of thousands of scientists in the world have done. Those who understand evolutionary theory ALL have waaaay better spelling and grammar skills than you do. I know it doesn’t appear obvious that one must be decent at spelling and grammar to know about evolution, but it really is so. The correlation (look up that word) is very strong, and by writing something like this on the internet with tons of spelling and grammatical errors really just makes you look like a total fool.

      Let me help you on your way a little bit:
      1) Capitalize. First letter in a sentence should be capitalized. That includes your name.
      2) Periods. Put a period at the end of every sentence (or a question or exclamation mark).
      3) ‘A’ before nouns that start with a consonant. ‘An’ before nouns that start with a vowel (like airplane).
      4) Learn the difference between replicator, replicating, replicate. It’s not arbitrary.
      5) Upgrade from the Creationists spell-checker to the standard spell-checker the rest of us use.
      6) “we know that a self replicate robot that made from dna need a designer” -> “We know that a self replicating robot that is made from dna needs a designer.” (Also, no we don’t know that. In fact we know this is not true at all, but this is a difficult thing that you can’t understand quite yet, and will have to wait until you have mastered grammar and basic science.)

      Then once in the far future when you have educated yourself a bit (a lot) more, you may realize that what you have written here is extremely puerile and naive, and have actually already been dealt with and refuted many times over by evolutionary biologists. Good luck and have fun!

      • bwana

        Bjørn, don’t be so hard on “gil”. He has a long process of evolution ahead of him/her… As he/she says “… small steps for milions years become a big steps.” :)

  5. Jeb

    “If I only had a TARDIS..”

    I just cheat and defy the laws of space and time. As long as I can relate an idea to something and start processing something starts working and I can eventual reject or confirm. Just need to get it in some understandable and familiar context. Does not matter what it is.

    I suspect a lot of this activity does not go on at a conscious level so whats happening on the surface is not the most important part. As long as the lights start flashing and the wheels and cranks start moving you don’t need to be aware of why you relate an idea to something else as long as you’re mind is moving something is going on and will emerge.

    I also think its good to rip thought from its moorings and fire in as many directions as possible. I refer to it as being out of time although can also be called being off topic.

    My first tentative experiment in using a different magic box and relating to science involved one from this collection.

    http://beingoutoftime.wordpress.com/2013/12/02/consumption/

    Bias and simply unknowingly making thought conform to pre- existing belief is an issue for everyone. Bjorn I don’t think insulting people who may view the world differently from you or I is helpful (I am more than capable of making the same error), whatever causes these issues and rifts it is certainly not stupidity unless you want to take a pretty blinkered, and simplistic take on these cultural issues.

    Certainly does nothing to get people engaging in a debate that can move beyond tribalism and ritual shit throwing and that’s no good for anyone no matter where you stand here. Although it clearly is appealing.

    • Jeb, if you are capable of “making the same error”, which was to not be good at spelling AND not understanding evolution + having the gumption to try to educate people who study evolution professionally, then I do declare that you also ought to be schooled in that case. Gil’s mistake is not to have a different view of the world, it is to not be educated and still think they have something or value to say to the rest of us.

      I know the tone was harsh, and I agree that it most likely antagonizes the intended recipient. However, there are always other people watching on the sidelines, and they need to know that a post like Gil’s has no place in any kind of serious debate about evolution. Whether Gil’s views are caused by stupidity (which I did not imply – I implied that (s)he is uneducated, which is not the same thing) is by the way an empirical question that you cannot dismiss without evidence.

    • Jeb

      Threat detection is somewhat error prone. No evolutionary disadvantage in mistaking a bush for a lion. Our small ape like but socially adapted brains have learned to manipulate such error for social advantage.

      I am sure both creationists and evolutionists are more than capable of getting creative here and make the important emotive need we have to very clearly identify the outlandish and infantile beliefs of other people.

      Important that appearances are maintained at all times. Identification must be presented in very simple black and white terms, that require no thought to grasp. Often the language of one is simply the mirror of the other.

      Both sides performing the same dance steps; lost and becoming an indistinct new entity in the shared embrace of dispute and its distinct dance moves.

  6. Jeb

    I can’t spell to save my life I am dyslexic. As a result I have plenty of experience of what you were implying. But I can read well as I have extensive educational experience in a range of subjects.

    “writing something like this on the internet with tons of spelling and grammatical errors really just makes you look like a total fool.”

    I think you have made some very unfortunate remarks.

    Jeb, if you are capable of “making the same error”…

    Deeply unfortunate.

    Although rather than beating you with a stick or taking offense (clearly unintentional and based on you’re assumptions with regard to eduction and spelling) I hope the comments may prove useful for you in future.

    “Gil’s mistake is not to have a different view of the world”

    “Bias and simply unknowingly making thought conform to pre- existing belief is an issue for everyone.”

    • Yes, I know about dyslexia and am aware that bad spelling does not necessarily imply that one is uneducated, but taken together with the facts that Gil isn’t educated about evolution either, and is merely reiterating creationist talking points that have been refuted, I made the (uncertain) claim that (s)he is uneducated. I hope that at at least some people got that it was an exasperated response to the same old tired thing that people dealing with creationists have seen a thousand times.

      • Jeb

        “I hope that at at least some people…”

        I am perfectly capable of grasping what you were trying to say and how you go about saying it.

        Wont add anything further. Really starting to get seriously “exasperated” for not too dissimilar reasons to you’re own.

      • Jeb

        Bjorn. Sorry if I sounded harsh. Perhaps unsurprisingly I get exasperated hearing people trot out the same beliefs with regard to this then attempting to justify them with appeals to empiricism. Its not on no matter how good the intention.

        I hope that at at least some people got that it was an exasperated response …

        I can grasp that fact as well not being foolish (most of the time). You are having a bad day with words I think. Perhaps not the best choice of words.

        • Jeb

          p.s I sometimes study the Fool in non-modern contexts. A sadly forgotten creature, modern usage is barren, simply a creature of abuse and dispute. I define the term slightly differently the issue the modern fool has is they know no error. Its always to be found in other people, never within where he resides in us all.

          No shame in being truly foolish and a creature of error, it is to learn.

  7. gil

    i again. actually english isnt my native.:)so this is because of this. the thing is that there is no step wise to a car from a self replicat material. so there is no step wise to a complex bilogic system also.

    • bwana

      Do you even realize how totally wrong your logic is!? Unless you don’t actually understand what you’ve written?

    • Ok, I apologize. It was meant to be funny, but as you are a non-native speaker it really doesn’t make sense what I wrote.

      However, your understanding of evolutionary mechanisms is poor/non-existent, so it remains that you need some education in that department.

      Cars do not evolve the same way as living organisms. You cannot compare them like you are. Different processes make them. You aren’t going to deny that babies cannot be made without a human putting their arms and legs and organs together, are you? That’s how cars are made, but babies are made without the aid of any intelligence. Babies of monkeys, for example. Living organisms have DNA, which cars do not. Completely different things = not comparable.

  8. gil

    hi again.i mean what if we will find such a car with dna? is that kind of car will be evidence for designer?

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