Pharyngula

How to make a snake

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First, you start with a lizard.

Really, I’m not joking. Snakes didn’t just appear out of nowhere, nor was there simply some massive cosmic zot of a mutation in some primordial legged ancestor that turned their progeny into slithery limbless serpents. One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.

What this means in a practical sense is that if you take a distinct form of a modern clade, such as the snakes, and you look at a distinctly different form in a related clade, such as the lizards, what you may find is that the differences are resting atop a common suite of genetic changes; that snakes, for instance, are extremes in a range of genetic possibilities that are defined by novel attributes shared by all squamates (squamates being the lizards and snakes together). Lizards are not snakes, but they will have inherited some of the shared genetic differences that enabled snakes to arise from the squamate last common ancestor.

So if you want to know where snakes came from, the right place to start is to look at their nearest cousins, the lizards, and ask what snakes and lizards have in common, that is at the same time different from more distant relatives, like mice, turtles, and people…and then you’ll have an idea of the shared genetic substrate that can make a snake out of a lizard-like early squamate.

Furthermore, one obvious place to look is at the pattern of the Hox genes. Hox genes are primary regulators of the body plan along the length of the animal; they are expressed in overlapping zones that specify morphological regions of the body, such as cervical, thoracic, lumbar, sacral/pelvic, and caudal mesodermal tissues, where, for instance, a thoracic vertebra would have one kind of shape with associated ribs, while lumbar vertebra would have a different shape and no ribs. These identities are set up by which Hox genes are active in the tissue forming the bone. And that’s what makes the Hox genes interesting in this case: where the lizard body plan has a little ribless interruption to form pelvis and hindlimbs, the snake has vertebra and ribs that just keep going and going. There must have been some change in the Hox genes (or their downstream targets) to turn a lizard into a snake.

There are four overlapping sets of Hox genes in tetrapods, named a, b, c, and d. Each set has up to 13 individual genes, where 1 is switched on at the front of the animal and 13 is active way back in the tail. This particular study looked at just the caudal members, 10-13, since those are the genes whose expression patterns straddle the pelvis and so are likely candidates for changes in the evolution of snakes.

Here’s a summary diagram of the morphology and patterns of Hox gene expression in the lizard (left) and snake (right). Let’s see what we can determine about the differences.

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Evolutionary modifications of the posterior Hox system in the whiptail lizard and corn snake. The positions of Hox expression domains along the paraxial mesoderm of whiptail lizard (32-40 somites, left) and corn snake (255-270 somites, right) are represented by black (Hox13), dark grey (Hox12), light grey (Hox11) and white (Hox10) bars, aligned with coloured schemes of the future vertebral column. Colours indicate the different vertebral regions: yellow, cervical; dark blue, thoracic; light blue, lumbar; green, sacral (in lizard) or cloacal (in snake); red, caudal. Hoxc11 and Hoxc12 were not analysed in the whiptail lizard. Note the absence of Hoxa13 and Hoxd13 from the corn snake mesoderm and the absence of Hoxd12 from the snake genome.

The morphology is revealing: snakes and lizards have the same regions, cervical (yellow), thoracic (blue), sacral (or cloacal in the snake, which lacks pelvic structures in most species) in green, and caudal or tail segments (red). The differences are in quantity — snakes make a lot of ribbed thoracic segments — and detail — snakes don’t make a pelvis, usually, but do have specializations in that corresponding area for excretion and reproduction.

Where it really gets interesting is in the expression patterns of the Hox genes, shown with the bars that illustrate the regions where each Hox gene listed is expressed. They are largely similar in snake and lizard, with boundaries of Hox expression that correspond to transitions in the morphology of vertebrae. But there are revealing exceptions.

Compare a10/c10 in the snake and lizard. In the snake, these two genes have broader expression patterns, reaching up into the thoracic region; in the lizard, they are cut off sharply at the sacral boundary. This is interesting because in other vertebrates, the Hox 10 group is known to have the function of suppressing rib formation. Yet there they are, turned on in the posterior portion of the thorax in the snake, where there are ribs all over the place.

In the snake, then, Hox a10 and c10 have lost a portion of their function — they no longer shut down ribs. What is the purpose of the extended domain of a10/c10 expression? It may not have one. A comparison of the sequences of these genes between various species reveals a detectable absence of signs of selection — the reason these genes happen to be active so far anteriorly is because selection has been relaxed, probably because they’ve lost that morphological effect of shutting down ribs. Those big bars are a consequence of simple sloppiness in a system that can afford a little slack.

The next group of Hox genes, the 11 group, are very similar in their expression patterns in the lizard and the snake, and that reflects their specific roles. The 10 group is largely involved in repression of rib formation, but the 11 group is involved in the development of sacrum-specific structures. In birds, for instance, the Hox 11 genes are known to be involved in the development of the cloaca, a structure shared between birds, snakes, and lizards, so perhaps it isn’t surprising that they aren’t subject to quite as much change.

The 13 group has some notable differences: Hox a13 and d13 are mostly shut off in the snake. This is suggestive. The 13 group of Hox genes are the last genes, at the very end of the animal, and one of their proposed functions is to act as a terminator of patterning — turning on the Hox 13 genes starts the process of shutting down the mesoderm, shrinking the pool of tissue available for making body parts, so removing a repressor of mesoderm may promote longer periods of growth, allowing the snake to extend its length further during embryonic development.

So we see a couple of clear correlates at the molecular level for differences in snake and lizard morphology: rib suppression has been lost in the snake Hox 10 group, and the activity of the snake Hox 13 group has been greatly curtailed, which may be part of the process of enabling greater elongation. What are the similarities between snakes and lizards that are also different from other animals?

This was an interesting surprise. There are some differences in Hox gene organization in the squamates as a whole, shared with both snakes and lizards.

i-fa000ad47d905c9af235e410cac479e7-nature08789-f1.2-thumb-400x212-42847.jpg
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Genomic organization of the posterior HoxD cluster. Schematic representation of the posterior HoxD cluster (from Evx2 to Hoxd10) in various vertebrate species. A currently accepted phylogenetic tree is shown on the left. The correct relative sizes of predicted exons (black boxes), introns (white or coloured boxes) and intergenic regions (horizontal thick lines) permit direct comparisons (right). Gene names are shown above each box. Colours indicate either a 1.5-fold to 2.0-fold (blue) or a more than 2.0-fold (red) increase in the size of intronic (coloured boxes) or intergenic (coloured lines) regions, in comparison with the chicken reference. Major CNEs are represented by green vertical lines: light green, CNEs conserved in both mammals and sauropsids; dark green, CNEs lost in the corn snake. Gaps in the genomic sequences are indicated by dotted lines. Transposable elements are indicated with asterisks of different colours (blue for DNA transposons; red for retrotransposons).

That’s a diagram of the structure of the chromosome in the neighborhood of the Hox d10-13 genes in various vertebrates. For instance, look at the human and the turtle: the layout of our Hox d genes is vary similar, with 13-12-11-10 laid out with approximately the same distances between them, and furthermore, there are conserved non-coding elements, most likely important pieces of regulatory DNA, that are illustrated in light yellow-reen and dark green vertical bars, and they are the same, too.

In other words, the genes that stake out the locations of pelvic and tail structures in turtles and people are pretty much the same, using the same regulatory apparatus. It must be why they both have such pretty butts.

But now compare those same genes with the squamates, geckos, anoles, slow-worms, and corn snakes. The differences are huge: something happened in the ancestor of the squamates that released this region of the genome from some otherwise highly conserved constraints. We don’t know what, but in general regulation of the Hox genes is complex and tightly interknit, and this order of animals acquired some other as yet unidentified patterning mechanism that opened up this region of genome for wider experimentation.

When these regions are compared in animals like turtles and people and chickens, the genomes reveal signs of purifying selection — that is, mutations here tend to be unsuccessful, and lead to death, failure to propagate, etc., other horrible fates that mean tinkering here is largely unfavorable to fecundity (which makes sense: who wants a mutation expressed in their groinal bits?). In the squamates, the evidence in the genome does not witness to intense selection for their particular arrangement, but instead, of relaxed selection — they are generally more tolerant of variations in the Hox gene complex in this area. What was found in those enlarged intergenic regions is a greater invasion of degenerate DNA sequences: lots of additional retrotransposons, like LINES and SINES, which are all junk DNA.

So squamates have more junk in the genomic trunk, which is not necessarily expressed as an obvious phenotypic difference, but still means that they can more flexibly accommodate genetic variations in this particular area. Which means, in turn, that they have the potential to produce more radical experiments in morphology, like making a snake. The change in Hox gene regulation in the squamate ancestor did not immediately produce a limbless snake, instead it was an enabling mutation that opened the door to novel variations that did not compromise viability.


Di-Po N, Montoya-Burgos JI, Miller H, Pourquie O, Milinkovitch MC, Duboule D (2010) Changes in Hox genes’ structure and function during the evolution of the squamate body plan. Nature 464:99-103.

Comments

  1. #1 formosus
    March 16, 2010

    First you start with a lizard

    All I could think of was Carl Sagan and “If you want to make an apple pie from scratch, you must first create the universe.”

    Indeed we are all nerds here.

  2. #2 Nerd of Redhead, OM
    March 16, 2010

    Wow, looks like the usual well explained science article, but I can’t read it until the morning. I know, it is morning where PZ is.

  3. #3 PZ Myers
    March 16, 2010

    No, it’s early afternoon. Had to take a break from pounding out ungodly text for the book.

    Now, back to it!

  4. #4 dreadpiratemick
    March 16, 2010

    Have you met any Australian snakes yet? Healesville has an excellent reptile house, if I recall correctly.

    The more of this genetics stuff I read the more annoyed I am at myself for choosing an arts degree. Fascinating.

  5. #5 John Morales
    March 16, 2010

    Wow.

    One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.

    That alone is worth “the price of admission”.

    Nice one, O pedagogue. Take a bow.

  6. #6 Nasherism23
    March 16, 2010

    Possibly the greatest blog post ever! Thanks PZ, this is why I love biology!

  7. #7 Phasic
    March 16, 2010

    And again, I have learned something.

    I had a fair idea that snakes and lizards were close, but it’s so interesting to hear about the mechanisms behind the similarities and differences.

  8. #8 tbfoster
    March 16, 2010

    Awesome article, will have to read it in its entirety after work (and after tonight’s talk over at MCC).

    Yeah, just turning 3pm here *yawn*. Question is are you stuck in a hotel room or have you found one of the many cozy cafe/lounges we have here to work in, PZ? Or one of the libraries? Lots of nice places to work/write, private or public.

  9. #9 Glen Davidson
    March 17, 2010

    I guess my plan of just cutting the legs off of a long lizard was a tad simplistic.

    Now what do I do with the lizard, though?

    Glen D
    http://tinyurl.com/mxaa3p

  10. #10 Brian
    March 17, 2010

    If you seek the means
    To make a snake,
    Pick some lizard genes
    To gently break.

  11. #11 Glen Davidson
    March 17, 2010

    Actually, I am curious. Is there any good comparison of the changes that occurred in snakes, and those that occurred, and are occurring, in legless and in reduced-leg lizards?

    I wonder how much the various legless lizards will converge with each other, and with snakes, in a few million years.

    Glen D
    http://tinyurl.com/mxaa3p

  12. #12 PZ Myers
    March 17, 2010

    The paper mentions that future research in burrowing snakes and caecilians would be useful, and also makes the point that limblessness is often associated with elongated bodies…further suggesting that changes in Hox patterning may be an enabling pre-pattern for modifying limbs.

  13. #13 tradewinds
    March 17, 2010

    PZ, we would forgive you if you ignored us for a while and got out and enjoyed yourself. LOL

  14. #14 tbfoster
    March 17, 2010

    He’s gotta have a break from drinking sometime during his visit :P

  15. #15 PZ Myers
    March 17, 2010

    Atheist, remember. We’re all grim, sullen drudges who find no joy in life.

    Although I am going to get together with Jamie Kilstein in a little bit and celebrate the Church of the Smiling Vagina. I’d tell you about the rites, but they’re secret.

  16. #16 raven
    March 17, 2010

    Legless lizard
    From Wikipedia, the free encyclopedia

    Legless lizard may refer to any of several groups of lizards which have independently lost limbs or reduced them to the point of being of no use in locomotion.[1] It is the common name for the family Pygopodidae[2], but often refers to other groups, such as limbless anguids, depending upon the region of the world.[citation needed] These lizards are often distinguishable from snakes on the basis of one or more of the following characteristics: possessing eyelids, possessing external ear openings, lack of broad belly scales, and/or a very long tail (while snakes have a long body and short tail).[1]

    Many families of lizards have independently evolved limblessness or greatly reduced limbs (which are presumably non-functional in locomotion), including the following examples:[1]

    Anguidae ? many limbless species, including genera Ophisaurus and Anguis.
    Cordylidae ? genus Chamaesaura.
    Pygopodidae ? members of the family are named Legless lizards due to their absent forelimbs and greatly reduced hindlimbs.[2] These are small flaps without digits, hence the common name “flap-footed lizards”.
    Dibamidae ? all members of the family are limbless burrowers which are nearly or completely blind.
    Anniellidae ? all members of the family are limbless.
    Gymnophthalmidae ? Many limbless and nearly-limbless species.
    Scincidae ? Many limbless and nearly-limbless species.
    Gerrhosauridae ? Several limbless or reduced-limbed species.

    The snakelike morphology has evolved many times. There are whole groups of lizards that have lost their external legs. Called rather imaginatively, the “legless lizards”.

    It would be interesting to compare the hox genes of these lizards with those of their ancestral lizard species and with their cousins the snakes.

    Great stuff. Someday we will know enough to build a dinosaur.

  17. #17 ronsullivan
    March 17, 2010

    Hot DAM# that was fun!

    And that’s the most detailed thing I have to say just now.

  18. #18 Glen Davidson
    March 17, 2010

    Cool. Thanks PZ and raven.

    Glen D
    http://tinyurl.com/mxaa3p

  19. #19 Antiochus Epiphanes
    March 17, 2010

    I had a phylogenetics professor who used to say “Snakes have legs. They just don’t have them anymore”* in reference to the synapomorphy shared by tetrapods…I guess, it would be better to say that snakes have legs, but they just don’t express them.

    Cool stuff. Will read the article fully when I am finished this accursed grading. Makes me feel crazy and angry.

    *He also used to say that dinosaurs weren’t extinct…he had just eaten some dinosaur McNuggets.

  20. #20 John Morales
    March 17, 2010

    Antiochus,

    I guess, it would be better to say that snakes have legs, but they just don’t express them.

    Which reminds me, whatever has been made of that snake with a leg report from China?

    I can’t recall hearing anything else since.

  21. #21 jaxkayaker
    March 17, 2010

    …squamates being the lizards and snakes together…

    and amphisbaenids! don’t forget the amphisbaenids!

  22. #22 boygenius
    March 17, 2010

    I guess my plan of just cutting the legs off of a long lizard was a tad simplistic.

    Glen D., please do tell me where to submit the bill for a replacement keyboard.

    Kind regards,

    BG

  23. #23 Rixaeton
    March 17, 2010

    Nice posting, PZ, and one of the wonderful things about science; always something more to know and understand. Now when I see a snake, I will think of it more as a misunderstood lizard :)

    And now, to show my snarky Atheist credentials, I have a general question: Does an angel loose its wings every time another gap that God occupied is closed?

  24. #24 https://openid.org/cujo359
    March 17, 2010

    OK, I have to ask – what do the d12 Hox genes do? Do they make legs grow? Was that something that was intuitively obvious to the casual observer and I missed it?

  25. #25 WowbaggerOM
    March 17, 2010

    Great post PZ, even for the non-scientists like me.

    I’ve loved snakes for as long as I can remember – actually, reptiles in general; apparently (I don’t really remember) my father took me to Taronga Park Zoo when I was three and then had to drag me away from the Komodo Dragon exhibit because I was so entranced. It’s probably contributes to why I love my copy of Douglas Adams’ Last Chance to See – it’s the hardcover with a picture of a dragon on the sleeve.

  26. #26 Jacob's Ladder
    March 17, 2010

    I’m suddenly very sorry that I’ve never had a proper biology class.

  27. #27 Jeanette Garcia
    March 17, 2010

    Gosh. This gives me a whole new conception of “junk in the trunk.” Elder learner here and loving it. Great post, PZ. I love it when you talk science.

  28. #28 johnlock
    March 17, 2010

    squamates have more junk in the genomic trunk

    The article (including any associated NSF grants etc) is fully justified by being able to summarise with that phrase IMO. :-)

  29. #29 Charlie Foxtrot
    March 17, 2010

    Woot! SCIENCE!
    I’m going to have to read this in the peace and quiet of the study tonight though – my simple IT brain needs some time to grox the Hox.

  30. #30 Phasic
    March 17, 2010

    Grokking the Hox will be helped by getting a lock on the Homeobox, then when you are feeling on top you can rock the SOX and pick the Pax and follow the Fox and see what develops.

    Word.

  31. #31 MadScientist
    March 17, 2010

    What a lovely story – such a pity it doesn’t really work because Evolution is Just a Theory ™. Or so I was told by a primitive lifeform that worships an imaginary friend.

  32. #32 DrivenB4U
    March 17, 2010

    nice! Pinch that one off on your coffee break Professor?

  33. #33 tdanielmidgley
    March 17, 2010

    Glad you ran into Jamie after the convention. If this religion becomes popular, I think the days of the Flying Spaghetti Monster may be numbered. And we can expect some more interesting t-shirts.

    Keep writing! The book will cement your Fifth Horseman status.

    Daniel

  34. #34 tbfoster
    March 17, 2010

    I’m wondering if it’d be too weird if I printed out a copy of this article and got PZ to sign it…going a bit too far maybe?

  35. #35 Janet Holmes
    March 17, 2010

    I love it when things don’t go as you would predict! The hox 10 genes ‘ought’ to have been shut down so the ribs could keep on coming, instead they’re more active and snakes grow extra ribs anyway, sooo cool!

  36. #36 Charlie Foxtrot
    March 17, 2010

    Damnation Phasic! Just add some pictures and you can read that to the kids at bedtime! :)

  37. #37 Sven DiMilo
    March 17, 2010

    who wants a mutation expressed in their groinal bits?

    You really ought to know beter than this by now, dude.

    The ‘slow-worm’ in the phylogeny Fig. is Anguis, a legless anguid lizard. Search Tet Zoo for that one, one of Darren’s favorites.

    Note re raven’s ‘kipedia quote: they forgot amphisbaenians, though not all of them are completely limbless…I give you the mighty mighty Bipes!

  38. #38 FossilFishy
    March 17, 2010

    THIS, this right here gives me hope. When the willfully ignorant have dragged my spirits down to the point where I wonder what will become of humanity, articles like this one are the antidote.

    Sure, I don’t understand it completely, I have to look words and concepts up. But as I do so and the picture becomes clearer I get the most incredible feeling. In the most extreme cases I get goosebumps, actual physical effects. They come from the joy of my newfound understanding and my appreciation of humanity’s incredible ability to increase it’s knowledge of the universe.

    Thank you PZ. And thank you to all you science folks who push back our ignorance, you are the light and hope of humanity.

  39. #39 Ichthyic
    March 17, 2010

    who wants a mutation expressed in their groinal bits?

    strange, but I keep getting all these emails implying a mutation to my groinal bits might be just the ticket.

  40. #40 Sven DiMilo
    March 17, 2010

    The ‘slow-worm’ in the phylogeny Fig. is Anguis, a legless anguid lizard.

    …point being, there’s evidently more than one way to make a legless squamate.

  41. #41 Pope Bologna XIII - The Glorious High Sauceror of Pastafarianism and Grand Poobah of His Holy Meatba
    March 17, 2010

    Wonderful afternoon reading. A day where nothing is learned is a day wasted.

  42. #42 Sven DiMilo
    March 17, 2010

    I’ve been perusing Fig. 2 hoping for some insight on the correct phylogenetic placement of turtles, but it doesn’t seem to be much help. As I read it, mammals, turtles, and the tuatara retain what I presume is the ancestral condition for amniotes, with some subtle regulatory changes in birds and all-hell broke loose in squamates (the Other DiapsidsTM). Turtles have a unique transposon that would be a smoking gun if found elsewhere…I totally want to see the situation in crocs.

  43. #43 apsalar
    March 17, 2010

    Was this inspired by a commenter at Balloon Juice who was wondering how to turn a lizard into a snake as an (apparently) well-intended question about how evolution works?

    I’m glad you’re also into the eastern hemisphere at the moment, PZ. I’m in China for 2 weeks, and every time I go to Google Reader during the daytime, I’m sad to see so few updates.

  44. #44 scooterKPFT
    March 17, 2010

    I just understood the role of religion this week because my friend, who is my age just lost his only child, who committed suicide.

    I can’t imagine this level of grief and I would want to believe in an afterlife.

    My friend suffers, but he is still rational, and knows his child is gone forever, which is the courage we share as atheists.

    Being an atheist is a hard road and that hard road is filled with pain theists will never understand.

    When you’re dead, you’re gone, it’s over.

    Nobody ever recovers from losing a child, there is no Jesus and no God and when you die you are dead.

    I always knew this, but never thought about it because my kids are all right.

    But I can understand why people cling to religion.

  45. #45 Sven DiMilo
    March 17, 2010

    How to make a snake

    Suggestions for the sequel:

    How to bake a cake
    How to take a brake
    How to stake a crake
    How to fake a drake
    How to flake a hake
    How to slake a jake

    etc.

  46. #46 scooterKPFT
    March 17, 2010

    How to slake a jake

    One man’s slake is another mans fake, all he lost he will retain,
    or ache
    or whatever rhymes

  47. #47 Sven DiMilo
    March 17, 2010

    scoot, thanks for sharing (not sarcastic)

    but…why here, in a hox-genes thread?

  48. #48 scooterKPFT
    March 17, 2010

    why here, in a hox-genes thread?

    I’m freaked out, I can’t handle this, this was a really cool kid, we used to trade riffs on the violin, and piano, which were skills we shared, and he just blew his brains out.

    I don’t have anybody else to talk to. I have my own live kid sitting around piking on the computer, but he doesn’t remember, and he hasn’t lost any people yet, he’s only 12, and he is a total slacker, he would never do that.

  49. #49 scooterKPFT
    March 17, 2010

    ain’t often right, but I never been wrong, seldom turns out like it does in the song

  50. #50 https://openid.org/cujo359
    March 17, 2010

    scooterKPFT @ 44 – That’s one of the things that is scary to me about such religions. They will cling onto a belief, no matter how irrational, if it promises that they get to see a loved one again.

    Sorry for your friend’s loss. Nothing will ease the pain but time, and even time won’t make it go away.

  51. #51 Sven DiMilo
    March 17, 2010

    I really meant why this thread rather than why Pharyngula–teh Thread Everlasting is many things to many people.

    But yeah, I know exactly how freaked out you feel. A young person’s suicide is a f*cking sh*tty thing to deal with for everybody…as a parent I can’t even begin to wrap my brain around it at all.

    And f*ck euphemism week…now it’s flagging my usual work-around html trick. You need asterisks, PZ? Repost.

  52. #52 Peter Ashby
    March 17, 2010

    @Raven

    Building something dinosaur shaped should not be too much of a problem. The tricky bit will be building functional dinosaur cells with the right biochemistry and there is only so much we are going to learn about that from birds. Then we need to recreate a dinosaur habitat (no grass for eg) and all their commensals. Now where were all those dinosaur bacteria and parasites stashed do you think?

    We know how to raise birds to be properly imprinted on parents using puppets so theoretically we could do it for a dinosaur. Might be tiring operating a herd of animatronic sauropods for, how long does it take for a sauropod to grow up?

    And while we are at it maybe we can find the time to conserve some elephant habitat?

  53. #53 Fred The Hun
    March 17, 2010

    Jeez! Next you’re gonna tell us that whole Eve apple and snake story was not quite the way it is told in Da Bible or sumthin.

    Like this Lizard ran out on the branch of a Malus orientalis tree and this Female ape like creature came over and couldn’t quite decide if she wanted to play with the lizard or eat the fruit of the tree. Then there was this bolt of lightning that hit the tree and set it on fire and next thing ya know the whole world was covered with god fearing Thor followers…

  54. #54 Fred The Hun
    March 17, 2010

    scooterKPFT @ 44

    As a father to an only son who is a teenager I find it even hard to think about it. I hope your friend has a very good social network in case he needs it.

    Best!

  55. #55 shonny
    March 17, 2010

    Posted by: Sven DiMilo Author Profile Page | March 17, 2010 4:18 AM

    How to make a snake

    Suggestions for the sequel:

    How to bake a cake
    How to take a brake
    How to stake a crake
    How to fake a drake
    How to flake a hake
    How to slake a jake

    etc.

    How to wake a fake?

  56. #56 Cowcakes
    March 17, 2010

    Wooohoo Science. But will have to wait till after getting my DGHI (Daily Geek humour intake) with the IT crowd or I will be too distracted

  57. #57 keenacat
    March 17, 2010

    squamates have more junk in the genomic trunk

    So full of win!

    Also, awesome article. Reminded me why I love genetics. This is so aaaaaawesome! How anyone would want to replace this piece of WIN and amazement that is genetics and genomics with Gawddidit is beyond me.

  58. #58 Haruhiist
    March 17, 2010

    Posted by: Sven DiMilo Author Profile Page | March 17, 2010 4:18 AM

    How to make a snake

    Suggestions for the sequel:

    How to bake a cake
    How to take a brake
    How to stake a crake
    How to fake a drake
    How to flake a hake
    How to slake a jake

    etc.

    How to slay the rake? (only to be done by oranges of course)

  59. #59 Kel, OM
    March 17, 2010

    What are you doing explaining biology PZ? Since you are an outspoken atheist, all you are doing is driving the moderates away through your association with an idea that the American public simply can’t handle. If you want to sell evolution, you need to not talk anymore…

    /moonenbaum

  60. #60 Zernk
    March 17, 2010

    I prefer The Far Side explanation: God rubbing Pla-Doh between his vertical palms and saying “Hey! These are EASY!”

  61. #61 IanM
    March 17, 2010

    All that biology without mentioning the glory of God?

  62. #62 Sven DiMilo
    March 17, 2010

    How to slay the rake? (only to be done by oranges of course)

    dog help me, I got that reference

  63. #63 JerryM
    March 17, 2010

    non-biologists question here, but I was wondering:

    Does a phylogenetic tree look different when focussing only on certain genes?
    ie, can you get different trees when focussing on different genes or gene pairs/clusters?

    If so, what insights would that bring?

  64. #64 Naked Bunny with a Whip
    March 17, 2010

    who wants a mutation expressed in their groinal bits?

    That depends on whether or not it involves bioluminescence.

  65. #65 Icarus
    March 17, 2010

    Fascinating article. I sometimes think about evolution and reflect on how amazing it is that the process keeps coming up with really useful new structures and functions for living organisms – it’s not always easy to see how such ‘clever’ adaptions could just ‘happen’ (as a creationist would probably put it). They would probably argue that “all mutations are damaging!” (or virtually all) but I have an inkling that they might actually be right about that in a sense, but wrong about the implications for evolution.

    In this article we can see how the Hox 13 genes have been somewhat ‘broken’ in the snake lineage – they are indeed damaged in the sense that they no longer perform the same as they did in ancestral species, but what could have been a disadvantageous deformity in other circumstances has actually helped to give rise to a whole new (and very successful) group of organisms.

    I think this must happen a great deal in evolution – genes are ‘damaged’ by mutation so that from our perspective we might say that their original function is impaired, but at the same time it may lead to opportunities for novel forms of life.

    I think of the human tail in this way too. If a monkey was born without a tail we would instinctively regard this as a congenital deformity – as damage to its genome, caused by mutation – but this is exactly what *must* have happened at some point in our evolutionary past (perhaps gradually over many generations), and we wouldn’t regard our current tail-less state as being disadvantageous or a deformity.

    So yes, perhaps most mutations *are* damaging to the genes they occur in, by curtailing their original function, but that doesn’t necessarily equate to them being disadvantageous – they may actually end up being extraordinarily beneficial.

  66. #66 Sven DiMilo
    March 17, 2010

    JerryM:
    Yes, different genes give different trees. Homoplasy (evolutionary convergence and reversal) happens. A lot. It’s messy and complicated and a big pain in the ass.
    That’s why the more data (genes, characters, taxa), the merrier.

  67. #67 KyBoiler
    March 17, 2010

    The bashing of our fellow bat guano crazy humans will never get old, but this post reminded me of the excellence of your scientific explanations too. More science!

  68. #68 Epinephrine
    March 17, 2010

    Has anyone looked at patterns of Hox gene expression among the various limbless vertebrates (glass lizards, caecilians, snakes, etc) to compare them? I wonder whether there is more than one way to make a snake.

  69. #69 llewelly
    March 17, 2010

    Some spelling fixes:

    For instance, look at the human and the turtle: the layout of our Hox d genes is vary similar …

    vary => very

    illustrated in light yellow-reen

    reen => green

  70. #70 Charlie from NoGodBlog
    March 17, 2010

    Happy Saint Patrick “chase the evil snakes that used to be serpents that god created out of Ireland” Day

  71. #71 Cowcakes
    March 17, 2010

    “Naked Bunny with a Whip”

    That depends on whether or not it involves bioluminescence.

    I remember a mates bucks night which involved bioluminescnce and his groinal bits.

  72. #72 Rick Miller
    March 17, 2010

    I had to look up the word “clade”. This is the first time I have ever seen it but it’s such a significant unit of classification!

    More people should know what a “clade” is. This word needs to be promoted.

  73. #73 Rikaishi
    March 17, 2010

    Scooter: back in junior high school, a friend of mine killed himself. The kid was brilliant, a comedian that could make a test-tube shriek like a banshee (this was deeply impressive to my 12-year old self at the time). His death hit the whole family pretty hard.

    I can tell you that it’s probably going to cast a pall on the rest of your year, and the funeral will be the worst you’ll ever attend. Everyone’s crying, and none of the usual words of comfort apply.

    As a kid, the only comfort I had was knowing that some good might come of it. That lessons would be learned by everyone. I learned that suicide is never an option, that our most brilliant children are often the most fragile, and there are more people who care for you then you know.

    Time heals, but you never forget. And I’ve never stopped learning from that experience.

    - – -

    When these regions are compared in animals like turtles and people and chickens, the genomes reveal signs of purifying selection ? that is, mutations here tend to be unsuccessful, and lead to death, failure to propagate, etc., other horrible fates that mean tinkering here is largely unfavorable to fecundity (which makes sense: who wants a mutation expressed in their groinal bits?).

    I’m given to understand that this is also the reason why our groinal bits smell like fish – the reproductive chemistry has seen very little change since we flopped out of the ocean oh-so-many million years ago.

    and we wouldn’t regard our current tail-less state as being disadvantageous or a deformity.

    I disagree. Google “catgirl”

  74. #74 Dae
    March 17, 2010

    Do we know much about Hox gene regulation? I’d be curious to see a similar study at the next level up of regulation, and to know what other vertebrate groups (if any, to which I’d hazard a quick guess in the negative) display this amount of variability in Hox genes.

    My lack of university access to online articles is irritating, but will end in August (woohoo!). Also, amusingly, a Google search of PZ’s citation yields a first page entirely consisting in blog and atheist website links.

  75. #75 Stephen Wells
    March 17, 2010

    @63: you can get some interesting results when you do phylogenies of genes that have duplicated.

    Suppose an ancestral species had a gene A which got duplicated and slightly altered so the ancestor has two genes, A and a.

    Generations later, this species divides into two. Both descendant species inherit genes A and a.

    Many more generations later, one descendant species has genes A’ and a’ ; the other descendant species has genes A* and a*.

    Gene a’ is more closely related to gene a* (in the other species) then it is to gene A’ (in its own species).

    Wrenching back to the point: on the broad scale, we get the same consensus phylogeny of life out of any gene. The details of branching order etc. are sometimes fuzzy because of effects like the above.

  76. #76 https://me.yahoo.com/a/DhjBEuJ8pt63x6eBKuPx0Jv9_QE-#7c327
    March 17, 2010

    Am I the only person here who read the recent book “How to Build a Dinosaur,” by Jack Horner and James Gorman?
    It’s a very similar proposal, except, of course, Horner wants to start with a chicken.
    Building a snake would be interesting, but building a T-Rex would be really way cool. Also, stupidly dangerous. I’m for it.

  77. #77 ppb
    March 17, 2010

    Now, now. Let’s give equal time to the Creationist’s viewpoint.

    Seriously though, another excellent article PZ.

  78. #78 RijkswaanVijanD
    March 17, 2010

    Good thing to read a really interesting post again..
    Eventhough I like the sect bashing, it seems too much a fornication sometimes.

  79. #79 christina.nicole.78
    March 17, 2010

    Very interesting, but one thing I find perplexing – why did this broken Hox gene survive in the squamates in the first place?

  80. #80 broboxley OT
    March 17, 2010

    excellent read. Have skinned snakes and often wondered why they were built that way. Going back to when they split I wonder what the evolutionary advantage would have been since there are snakes in all types of terrain and climate. Perhaps burrowing mammals were a favored food.
    thanx,
    bill

  81. #81 Celtic_Evolution
    March 17, 2010

    Hope nelis didn’t try to read this. You could probably hear the sound of his head popping half way around the world.

  82. #82 Lynn Wilhelm
    March 17, 2010

    Took my 1st grader to the NC Museum of Nat Sci for Reptile and Amphibian day.

    We saw some cool amphibians that resembled eels or snakes. One was a Siren (native in NC!)that only had front legs. The other was an aquatic salamander (don’t recall the name) with all four legs–that really didn’t look functional.
    Just wondering what’s happening with them evolutionarily speaking.

    I know it’s amazing, but I think we saw the elusive Transitional Species! They do exist, they do exist!!!1!11

  83. #83 geds81
    March 17, 2010

    I find this article extremely suspicious. Just the other day there was a discussion of exactly how to get the idea of a lizard becoming a snake across over at Slacktivist. The main point of the original person to bring it up was that they could not understand how the intermediate steps could happen or were beneficial and had never seen it explained well.

    And here’s PZ Myers, known reader of Slacktivist, writing a post on how to make a snake…

    Coincidence?

    I dunno. Could be. Seems PZ’s had a lot more important things to do than read the comments section of Slacktivist lately…

  84. #84 David Marjanovi?
    March 17, 2010

    More evo-devo genetics! Moremoremore! :-)

    Which reminds me, whatever has been made of that snake with a leg report from China?

    Had almost certainly swallowed a toad and burst. That happens; snakes even tend to survive it.

    Note how the leg is right in the middle of the snake? compare that to the first figure.

    I’ve been perusing Fig. 2 hoping for some insight on the correct phylogenetic placement of turtles, but it doesn’t seem to be much help. As I read it, mammals, turtles, and the tuatara retain what I presume is the ancestral condition for amniotes, with some subtle regulatory changes in birds and all-hell broke loose in squamates (the Other Diapsids?). Turtles have a unique transposon that would be a smoking gun if found elsewhere…I totally want to see the situation in crocs.

    Seconded!!!

    However, the chicken lacks that transposon, and turtles as crurotarsan archosaurs ( = closer to crocs than even the birds are) is very, very, very hard to imagine, even though some molecular analyses have found just that.

    I just understood the role of religion this week because my friend, who is my age just lost his only child, who committed suicide.

    I can’t imagine this level of grief and I would want to believe in an afterlife.

    And then I’d be even sadder, because I know that wishful thinking doesn’t make it so. :-|

    I had to look up the word “clade”. This is the first time I have ever seen it but it’s such a significant unit of classification!

    I wouldn’t even call that “classification”. It belongs to phylogenetics, the science of how to reconstruct evolutionary trees.

  85. #85 RijkswaanVijanD
    March 17, 2010

    Well.. Amphibian divergence is placed way before development of the trait, this is illustrated by the Xenopus (Clawed Frog)shown as an outgroup in the figure. This may implicate some degree of convergent evolution for the amphibians in question and snakes, not transition in my opinion.

  86. #86 Sven DiMilo
    March 17, 2010

    an aquatic salamander (don’t recall the name) with all four legs–that really didn’t look functional

    Amphiuma.
    Very eel-like indeed. They are most common in weed-choked ponds and swamps.

  87. #87 KOPD
    March 17, 2010

    I saw a glass lizard once (a kind of legless lizard). I told a friend about it and they asked “how is that not a snake?” I just said because it’s a lizard, but perhaps a better answer would have been to relate it to bats and birds.

  88. #88 David Marjanovi?
    March 17, 2010

    why did this broken Hox gene survive in the squamates in the first place?

    Probably it’s still doing something.

    And if not, getting completely rid of a gene isn’t easy, even though the snakes have managed to do it with HOXC12.

    Going back to when they split I wonder what the evolutionary advantage would have been since there are snakes in all types of terrain and climate. Perhaps burrowing mammals were a favored food.

    CELEBRITY DEATHMATCH!!!1!!11!

    Some think it’s for burrowing, or at least for slithering through dense vegetation (as seen in legless skinks today).

    Others think it’s for eel-like swimming. They (but not the other guys!) find the snakes to be closely related to the great & mighty mosasaurs and even more closely to animals like Adriosaurus (look it up).

    Most or all of the earliest known snakes, those that retained hindlimbs, did indeed live in the sea. The question is where on the family tree they lie; that’s part of the celebrity deathmatch.

    I suppose John Scanlon, FCD, will comment on this. He’s on one side of the celebrity deathmatch.

    The other was an aquatic salamander (don’t recall the name) with all four legs–that really didn’t look functional.

    The awesome three species of Amphiuma.

  89. #89 Sili
    March 17, 2010

    How to wake a fake?

    I’d rather fake my wake.

  90. #90 Egaeus
    March 17, 2010

    A second vote for glass lizards.

  91. #91 Nerd of Redhead, OM
    March 17, 2010

    Finally found the time to read PZ’s review. Excellent of course. And I want to know more. Alas, back to the job…

  92. #92 Anri
    March 17, 2010

    I am of the optinion that this post does not actually exist.

    I have been told repeatedly by a number of people who have read extensively through Pharyngula that PZ never, ever posts science on this ‘science’ blog, but only meanie-mouth invective against those holy ones who worship the one really truly-truey-true god. (And sometimes insults people who worship baddie-fake-falsy gods, too, but who cares about them – they’re probably dirty and ugly too.)

    And I’m certain that these people would never misrepresent anything.
    Not even once.

    Ergo, this whole thread is a figment of a fevered imagination.

  93. #93 IaMoL
    March 17, 2010

    So is it in our future that some technician(s) will be able to take a lizard ova and selectively hack those genes and make a snake or snake-like offspring? Or is that too Promethean to even whisper about?

  94. #94 IaMoL
    March 17, 2010

    Well, everyone is entitled to their optinion.

  95. #95 RijkswaanVijanD
    March 17, 2010

    It’s a kind of magic.. I know

  96. #96 David Marjanovi?
    March 17, 2010

    This may implicate some degree of convergent evolution for the amphibians in question and snakes

    Of course it does. Limblessness evolved several times completely independently.

    So is it in our future that some technician(s) will be able to take a lizard ova and selectively hack those genes and make a snake or snake-like offspring?

    That’s already possible today. It would just be a massive waste of time and money.

  97. #97 Lynn Wilhelm
    March 17, 2010

    Oh, I didn’t mean to sound like I thought the snake–like amphibians we saw were a transitional species that had anything to do with snakes.

    I was just trying to say that anything we see now could be/is transitional.

  98. #98 Lynn Wilhelm
    March 17, 2010

    that should be snake-like

  99. #99 Ewan R
    March 17, 2010

    #92

    Of course the post exists… there is however no science involved, everybody with half a brain (for real) knows that evolution isn’t science, but just a thinly veiled attack on religion, so frankly this post is business as usual.

  100. #100 Ian in OH
    March 17, 2010

    My kingdom for a HS biology lesson like this. (Grew up in WV so maybe I shouldn’t be too surprised.) Only had 1 biology course during HS. Included endless lessons, badly taught, about Mendel’s pea plants and dominant/recessive genes. The 3 chapters in the book concerning evolution, natural selection, and Darwin were simply skipped. No ID or creationism, but teaching as if Darwin never existed.

    Who knows? My bachelor’s in poli sci and history certainly hasn’t done anything for me.

  101. #101 IaMoL
    March 17, 2010

    I see Ewan is a Dunning-Kruger graduate.

  102. #102 ConcernedJoe
    March 17, 2010

    wow – worth the price of admission!!

    thanks for lesson Dr. Myers

    now question: do you know where DNA came from? (ok lame joke – devil made me make me !)

  103. #103 DLC
    March 17, 2010

    So there’s this whole DNA thing that people seem to conflate with “Divine Blueprints. ”
    If it were blueprints, every human being would look like This

  104. #104 Thebear
    March 17, 2010

    @IaMoL #101:

    Or just a confirmation of Poes law. Kinda hard to say (because of Poes Law of course).

  105. #105 SteveM
    March 17, 2010

    re 70:

    Happy Saint Patrick “chase the evil snakes that used to be serpents that god created out of Ireland” Day

    And to everyone in Boston, Happy Evacuation Day when all the evil snakes (British Redcoats) were chased out of the city.

  106. #106 SteveM
    March 17, 2010

    re 24:

    OK, I have to ask – what do the d12 Hox genes do? Do they make legs grow? Was that something that was intuitively obvious to the casual observer and I missed it?

    I too would like to know.

  107. #107 Menyambal
    March 17, 2010

    Great science, PZ, and great writing.

    This reminds me of the day I found a legless lizard down at Ozark National Scenic Riverways. I’m not a snake expert, but I’ve seen lots of snakes and lizards, so I knew what they look like, but didn’t know there were legless lizards around (and had little idea what they looked like). But when I found this guy, there was no doubt in my mind–he was a lizard, with a body like a snake.

    The head was obviously lizard, and the body wasn’t quite right for a snake, so I knew what it must be. But it was a surprise. And another confirmation of the wonder of evolution.

  108. #108 Ewan R
    March 17, 2010

    #101 and #104 – I’d hoped the parenthetical for real after half a brain would make things obvious (as anyone operating at 50% average mental capacity is probably more likely to agree with the rest of my statement)

    Apparently however my sense of humour sucks (although here I will claim that Dunning-Kruger applies!)

  109. #109 raven
    March 17, 2010

    Lynn W.:

    I was just trying to say that anything we see now could be/is transitional.

    wikipedia legless lizards, quoted in full in #16.

    Anguidae ? many limbless species, including genera Ophisaurus and Anguis.
    Cordylidae ? genus Chamaesaura.
    Pygopodidae ? members of the family are named Legless lizards due to their absent forelimbs and greatly reduced hindlimbs.[2] These are small flaps without digits, hence the common name “flap-footed lizards”.
    Dibamidae ? all members of the family are limbless burrowers which are nearly or completely blind.
    Anniellidae ? all members of the family are limbless.
    Gymnophthalmidae ? Many limbless and nearly-limbless species.
    Scincidae ? Many limbless and nearly-limbless species.
    Gerrhosauridae ? Several limbless or reduced-limbed species.

    There could well be classical transitional forms in the many independently evolved legless lizards.

    These are families except the (absent from this list) amphisbaenians which are a suborder and some claim to be “related to the lizards and snakes”.

    In some of the families, there are both legged, reduced legged, and leggless species. I suppose one could consider the reduced leg species to be “transitional”.

  110. #110 Thebear
    March 17, 2010

    @ EwanR:

    Do not underestimate the powers of Poes law.

    Or it was just my own mush-for-brains which made me incapable of seeing wheter it was a parody or not :)

  111. #111 IaMoL
    March 17, 2010

    #108
    *laughs*
    I reread it several times but the half a brain line seemed aimed at Pharyguloids. I’ve been engaged with several facebook friends who are of the evolution is just to refute God persuasion. It’s enough to make me want a lobotomy, if not a full hemispherectomy.

  112. #112 IaMoL
    March 17, 2010

    David Marjanovi?:

    That’s already possible today. It would just be a massive waste of time and money.

    I see I asked the wrong question. Is it possible to tinker with the snake’s DNA and create a lizard offspring which is actually a progenitor (a synthetic regression to an earlier form?)?
    It wouldn’t be just a smoking gun for evolutionary biology, it would put the bullet back in the cartridge in full view of everyone.
    Would it still be a massive waste of time and money?

  113. #113 raven
    March 17, 2010

    It wouldn’t be just a smoking gun for evolutionary biology, it would put the bullet back in the cartridge in full view of everyone.

    It wouldn’t make any difference to the religious kook creationists.

    Evolution was a fact and well proven theory a century ago. There is no evidence needed or possible that will convince Presuppositionalist creationists. They are immune to facts and reason.

    They set up goals like, “create life”. Then when they do, they simply move the goalposts. It is getting to the point now where their latest goal is to have scientists recreate the Big Bang.

    Humans are sometimes born with atavistic tails or covered with fur. The creationist reaction is amusing. They close their eyes, scream “I didn’t see that so it didn’t happen” and then forget it.

  114. #114 gr8hands
    March 17, 2010
  115. #115 Naked Bunny with a Whip
    March 17, 2010

    It is getting to the point now where their latest goal is to have scientists recreate the Big Bang.

    Which would, of course, just demonstrate that intelligent agency is required to create a universe.

  116. #116 David Marjanovi?
    March 17, 2010

    These are families except the (absent from this list) amphisbaenians which are a suborder and some claim to be “related to the lizards and snakes”.

    1) Whether something is a family or suborder or anything isn’t a fact, it’s a shaky convention.
    2) The amphisbaenians are very closely related to Lacertidae (Real True Old-World Lizards); more so than the skinks are.

    Is it possible to tinker with the snake’s DNA and create a lizard offspring which is actually a progenitor (a synthetic regression to an earlier form?)?

    Reverse-engineering? Maybe? except we wouldn’t have much of a way of testing how close the result would be to any actual unknown ancestor.

  117. #117 chukgoodin
    March 17, 2010

    Excellent article, love to see more science like this in Pharyngula.

  118. #118 otrame
    March 17, 2010

    @scooterKPFT

    I’m so sorry about your friend. Depression is a vicious disease.

    The worst part is that it is more or less natural for teens to be somewhat depressed at least some of the time and many of their responces to life-as-they-currently-view-it look much like depression. It’s so hard to tell when it has gone from that into serious, life threatening depression.

    Please keep an eye on your friend and recommend he get some temporary pharmacological help if he needs it.

  119. #119 'Tis Himself, OM
    March 17, 2010

    Enough boring science. Let’s get back to bashing Jains. ;-P

  120. #120 echidna
    March 17, 2010

    ‘Tis! Wash your mouth out with soap. Boring science indeed….

  121. #121 great.american.satan
    March 17, 2010

    This addresses something I’ve come to wonder about convergent evolution – If it’s more likely within a clade than without, what sorts of mechanisms for it could we find? The bat/whale echolocation discovery comes to mind.
    Another thing: If your HOX genes are all wacky and your species is mostly legless, could you re-develop sensible limbs in the future? Is it possible that’s why squamates have this condition? Maybe an ancestor lost its limbs, got sketchy DNA, then redeveloped in a way that wouldn’t be likely in lineages with more sensible HOX structure, leaving them flexible enough to alter limbs readily in the future.
    Maybe this has to do with how mosasaurs evolved, given that they were squamates and highly derived ones practically look like fish.
    I’m a fine arts major, so never mind me…

  122. #122 RijkswaanVijanD
    March 17, 2010

    “Of course it does. Limblessness evolved several times completely independently.”

    I know that, I was just making the point that limbless amphibians are not a transitional state as Lynn suggested..

    Go and feed the rooster or something

  123. #123 TheBlackCat
    March 17, 2010

    The paper mentions that future research in burrowing snakes and caecilians would be useful, and also makes the point that limblessness is often associated with elongated bodies…further suggesting that changes in Hox patterning may be an enabling pre-pattern for modifying limbs.

    I would also be interested in seeing a comparison between “normal” snakes to snakes that do have pelvic structures.

    Also, although snakes did not descend from modern lizards, looking at the family tree anoles (one type of lizard) or more closely related to snakes than they are to geckos (another type of lizard). This would indicate that they evolved from an animal that was, from a cladistics sense, a type of lizard, which would mean that snakes are also a type of lizard, wouldn’t it? In other words, some lizards have a more recent common ancestor with snakes than they do with other lizards. Saying that snakes are not lizards would be like saying people are not apes, and saying that the animal snakes evolved from was not a lizard would be like saying the animal we evolved from was not an ape.

  124. #124 Psalmotoxin
    March 17, 2010

    Great explanation – I read that earlier this and enjoyed it very much – Nature must be having a thing about snakes, this article is a bit more in my field, all about infraread detection by snakes:

    http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature08943.html

  125. #125 David Marjanovi?
    March 17, 2010

    Another thing: If your HOX genes are all wacky and your species is mostly legless, could you re-develop sensible limbs in the future?

    In principle, yes, as long as enough of the rest of the machinery is left.

    For instance, birds (or chickens at least) can’t get their teeth back, because some of the genes for enamel proteins are broken and others can’t be found at all.

    Is it possible that’s why squamates have this condition? Maybe an ancestor lost its limbs, got sketchy DNA, then redeveloped in a way that wouldn’t be likely in lineages with more sensible HOX structure, leaving them flexible enough to alter limbs readily in the future.

    That’s even more highly unparsimonious than the alternative.

    Maybe this has to do with how mosasaurs evolved, given that they were squamates and highly derived ones practically look like fish.

    Why? All mosasaurs retained both limb pairs (as flippers). A certain amount of body elongation did take place, but that’s it.

  126. #126 the_manxome_foe#a0503
    March 17, 2010

    Note re raven’s ‘kipedia quote: they forgot amphisbaenians, though not all of them are completely limbless…I give you the mighty mighty Bipes!

    That has to be one of the cutest little critters I’ve ever seen.

    Made my morning that did.

  127. #127 great.american.satan
    March 17, 2010

    “Why? All mosasaurs retained both limb pairs (as flippers). A certain amount of body elongation did take place, but that’s it.”
    Well, I did say to ignore me as I’m a fine arts major, but I was thinking modification of limbs into flippers could happen more quickly if the genetic regulation of your limb’s structure is more elastic than in mammals, for example, but it was a lousy point for other reasons besides (see mammals with normal HOX genes evolving flippers at least three separate occasions), so I retract it.
    -

  128. #128 shiftyeyedog
    March 17, 2010

    Sir, this whole entry is blasphemy. God made snakes as you can see here: http://student.vub.ac.be/~pprovinc/images/godmakessnake.jpg

    Hail the prophet Larson!

  129. #129 Kirk
    March 17, 2010

    It must be why they both have such pretty butts.

    Definitely not enough discussion thus far on this.

    Now when I see a snake, I will think of it more as a misunderstood lizard :)

    Now when I see a snake, I will think about how it wishes it had a butt as pretty as a turtle.

  130. #130 jaxkayaker
    March 17, 2010

    Posted by: Sven DiMilo | March 17, 2010 2:46 AM
    .
    .
    .
    Note re raven’s ‘kipedia quote: they forgot amphisbaenians, though not all of them are completely limbless…I give you the mighty mighty Bipes!

    Sven – since the Wikipedia article raven quoted is about legless lizards, not legless squamates generally, they didn’t forget amphisbaenians, which are squamates, but not lizards.

    Under the taxonomy I learned in herpetology class 17 years ago, there are three suborders in the Order Squamata, the common names for those three suborders are lizards, snakes and worm-lizards (amphisbaenids or amphisbaenians).

  131. #131 cdmissinglink46
    March 17, 2010

    “One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology”

    Great summary statement. Pardon my ignorance but looking for an education. My understanding is that there are 1400 genes that are different between the human and the chimp. I am not sure if we can even predict what that means in regards to the difference between modern man and the H-C common ancestor. With the knowledge that neutral drift drives most evolutionary change, can we predict how many different species would be between us the the common ancestor? has there been any evidence of a macroevoltionary event? Just trying to keep up. thanks for the info if anyone has time.

  132. #132 finback
    March 17, 2010

    I’ve often tried to figure out the phylogeny of snakes and lizards, and have (based on my own ideas/reading) got a rough model. Sadly, I’m sure my formatting to try to convey it won’t work, so I’mma interrupt myself here to break it down to a quicker format
    Varanidae (the goannas)
    Mosasauridae (big marine lizards, close to varanids)
    Aigalosauridae (freaky skinny little mosasaur-kin, with reduced feet, I’m thinking they probably evolved to exploit coral reefs with that body form)
    early marine snakes (eg Haasiophis, Pachyrachis)which still had their tiny nubbin-legs
    snakes en-masse

  133. #133 broboxley OT
    March 18, 2010

    @cdmissinglink46 #131 cant resisr
    “mmm thats a good looking monkey”
    /me flees

  134. #134 Ewan R
    March 18, 2010

    #131 – I think it would depend on what timescale you chose to sample on – if you decided you were going to look back every 1000 years and see if interbreeding could occur between time X and time X -1000 years then my guess is the number of species between us and the common ancestor with chimps would be 1 (ie no new species) – species is a relatively arbitrary definition particularly when you start attempting to apply the distinction across time (it’s easier across large timescales, but the ability to apply over small timescales falls apart)

  135. #135 Sven DiMilo
    March 18, 2010

    With the knowledge that neutral drift drives most evolutionary change, can we predict how many different species would be between us the the common ancestor? has there been any evidence of a macroevoltionary event?

    Hmmm. Most evolutionary change at the level of single-nucleotide polymorphisms is due entirely to drift, and some evolutionary change at the level of amino acid sequences is probably due to drift, but a lot has been driven by selection as well. I think Ewan R is correct that it’s more accurate to think of a single unbroken lineage (identifiable, though, only in hindsight) in which speciation, if any, is gradual and continuous and seamless anagenesis, while populations keep splitting off that lineage, some to evolve into separate species (cladogenesis). What confuses a lot of people is the idea that we are extremely unlikely to find fossilized members of the unvroken lineage, and far, far more likely to have found branch-populations.

    In any event, fossils like Ardipithecus and Lucy suggest no single huge macro-event.

  136. #136 Sven DiMilo
    March 18, 2010

    Under the taxonomy I learned in herpetology class 17 years ago, there are three suborders in the Order Squamata, the common names for those three suborders are lizards, snakes and worm-lizards (amphisbaenids or amphisbaenians).

    Problem is, as pointed out above, both ‘snakes’ and ‘amphisbaenians’ are phylogentically nested solidly within the much larger ‘lizards’, so the classical taxonomy (which I also learned…more than 17 years ago!) doesn’t make any sense evolutionarily. Much has been learned in the last 17 years, and modern taxonomy is abandoning Linne’s confining conventions of classes, orders, and families and substituting a less-corsetted dose of reality.

    But I’m sure you are correct as to why amphisbaenians were (incorrectly) left off the ‘kipedia list.

  137. #137 Pacal
    March 18, 2010

    Repeated Sexual Intercourse! Wow!!

  138. #138 monado
    March 19, 2010

    I’ve seen lizards in a pet shop that had weak little legs. They were called “grass lizards” and had brown backs with lighter, lengthwise stripes so that they looked like garter snakes. I have no idea of the species.

  139. #139 jaxkayaker
    March 19, 2010

    Sven – even under a cladistic regime of taxonomy, we would still have non-clade grades informally known as lizards, snakes and amphisbaenids. The overall clade and grade could still be Squamata. Though from a strict phylogenetic viewpoint the lizard group is paraphyletic, it would be easily understood that lizards are non-snake, non-amphisbaenid squamates.

  140. #140 John Scanlon FCD
    March 22, 2010

    Finback #132, you’ve nearly caught up with where Ferenc Nopcsa was at in 1923, or Sam McDowell in 1954. What’s missing is the ‘dolichosaurs’, a whole string of more-or-less intermediate, somewhat elongated and somewhat limb-reduced aquatic forms along the stem between the aigialosaur-mosasaur clade and the hyper-elongate, totally armless and shoulderless snakes. David M mentioned Adriosaurus above, but there are quite a few more of these little guys, almost all from the Cenomanian (~93-99 million years ago), and now known (at least by the odd vertebra, but sometimes complete skeletons) from most parts of the world. Unfortunately, none of them so far has the skull really well enough preserved (or at least exposed) to check most of the characters that would test continuity between conditions in mosasauroids and snakes, but I expect we’ll be seeing hi-res CT scans of Pontosaurus and some others in the next couple of years.

    Goannas (or monitors, Varanidae) do look – morphologically and behaviourally – like an excellent snake sister-group or quasi-ancestor, but the molecular evidence doesn’t find this to be the case; instead, they’re nested within the clade Anguimorpha which – to my surprise – doesn’t seem to actually include snakes (but forms the sister-group to snakes). Other anguimorphs are much more ‘regular lizards’, so (apparently) the many derived similarities of gioannas and snakes are either convergent (the boring answer) or are actually ancestral anguimorph characters, some of them secondarly lost in anguids, xenosaurs etc.

    There’ve been claims that anguimorph monophyly (excluding snakes) refuted the snake-mosasaur relationship AND the aquatic ancestry of snakes, but that is simply bullshit (have they got DNA from mosasaurs yet?; or have they found new mosasaur-varanid synapomorphies not shared by snakes? – nope). As in any CELEBRITY DEATHMATCH!!!1!!11! there’s one side that can sometimes be characterised as ‘denialists’, i.e. the headline claims in their papers are logically disconnected from the data they actually present, but seek to dichotomise what we evidence-based scientists see as a continuum. [Google 'BANDit + MANIAC' for similar examples]

    The Hox-gene paper that PZ riffed on (‘junk in the genomic trunk’ – love it) is also only part of the story: only a small number of squamates are included, with only one snake, but there are obviously a lot of changes to identify and place on the phylogeny, which will take a lot more work. All those LINE and SINE characters are excellent material for building the phylogeny, whatever else they’ve been up to in altering gene control and function, so I hope they’ll soon be sequenced in a bunch of anguimorphs and other lizards, and a spread of snake lineages too. There are people looking at origin of snake-like characters (elongation and limb-loss) in various lizard groups, one of the busiest being the Australian skink genus Lerista which has scores of species ranging from fat, strong-limbed surface lizards to snake-like sand-swimmers, and multiple losses of limbs and digits.

    Sorry for the tl;dr factor here; I haven’t managed to sign in to comment for quite a few months. Rain again after a dry spell (literally here in NW Qld, ex-cyclone Ului nipped across from the coast in record time…)

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