Pharyngula

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This is an amphioxus, a cephalochordate or lancelet. It’s been stained to increase contrast; in life, they are pale, almost transparent.

i-56ee51e328b10451feb168cd9bab0ea5-amphioxus.jpg

It looks rather fish-like, or rather, much like a larval fish, with it’s repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.

i-e961343b9bf5b6dfd74823fba6deeafb-amphioxus_closeup.jpg

It’s not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.

But first, a little question that needs to be resolved. This is an ascidian, a member of the subphylum urochordata.

i-ec680dba6f32c0edb3b22a2f0ba110bc-ascidian-amphioxus.jpg

Like us and like amphioxus, it also has a central notochord, and it also has segmental blocks of muscle and a dorsal nerve cord, and in this case you can also see that it has an expansion of the front of the nerve cord into something that looks rather brain-like. Ascidians are also more diverse and successful than the cephalochordates.

A major difference, though, is that amphioxus maintains its chordate morphology throughout its life — the picture at the top of this page is an adult. Ascidians, on the other hand, only look like tadpoles in their larval stages, which is only a dispersal form. They swim away from their parent and settle down on a solid surface and throw away their tail and brain and squat permanently as a sessile filter feeder called a sea squirt. This opens a debate about chordate ancestry. Did we 1) evolve from an ascidian-like animal, that maintained it’s larval stage throughout life and refined its form to become something like an amphioxus, which then evolved into the vertebrates? Or was 2) an amphioxus-like animal at the base of the family tree, and the ascidians are the weird cousins who went off and evolved a specialized adult form?

I’ve discussed ascidian evo-devo before, and the consensus so far is that the second model is most likely, and ascidians are a highly derived descendant of the last common ancestor of all chordates, which have gone off in some radical and very interesting directions. The current paper on the amphioxus genome confirms that, and in particular reveals an interesting fact: while the ascidian genome has undergone some major remodeling that makes it very different from our own, the amphioxus genome seems to have conserved many ancestral features and may very well be a good proxy for examining the genetics of the last common chordate ancestor.

Before we move on to the genetics, though, look at the diagram above. At the bottom are two embryos at the 8-cell stage, with the prospective fates of some regions marked: cells that form in the area with the horizontal hatching will become notochord, and those with the vertical hatching will become the neural tube. The two are very similar; the one on the left is an ascidian embryo, and the one on the right is an amphioxus embryo. Both exhibit a pattern of mosaic development, in which the fates of regions of the egg are mapped out by a pre-pattern of molecular determinants. Vertebrates do not do this, or do so to a much lesser degree; we have regulative development, in which early cells are much more plastic, and gradually and progressively determine their role in the embryo. This suggests, though, that mosaicism may be an ancestral property of the chordate lineage, and we are the weirdos who have departed far from the traditional pattern in this regard.

Let’s also have a brief video interlude. Below is a time-lapse movie of amphioxus development. You’ll see the 8-cell stage illustrated above, and then it flies through a series of transformations into a hollow ball, folding in a portion of the structure to make a cup-shape organism, then elongating to make a kind of canoe-shaped beast, which then differentiates the various muscles and tissues to make an embryonic amphioxus. Isn’t it lovely?

The recent paper in Nature by Putnam and others describes the completion of the draft genome sequence for the amphioxus species, Branchiostoma floridae. The genome is about 520 megabases long (a sixth the size of ours) and contains about 22,000 protein coding regions, or genes, and so is about the same size as ours. All this data means that a better phylogenetic tree can be assembled, which is shown below and which supports the conclusion that amphioxus diverged early in chordate history, followed by a later split between the urochordates and the vertebrates.

i-9c44fde03abe30b724874bc7d8eff83e-chordate_clade.jpg
(click for larger image)

Deuterostome phylogeny. Bayesian phylogenetic tree of deuterostome relationships with branch length proportional to the number of expected substitutions per amino acid position, using a concatenated alignment of 1,090 genes. The scale bar represents 0.05 expected substitutions per site in the aligned regions. Long branches for sea squirt and larvacean indicate high levels of amino acid substitution. This tree topology was observed in 100% of sampled trees. Numbers in red indicate bootstrap support under maximum likelihood. Unlabelled nodes were constrained.

Look at the magnitude of the substitutions in the urochordates! If you want to argue that any chordate group is “more evolved” than any other, you’d have to hand the title to those somewhat obscure organisms — they’ve been shedding genes and reorganizing and adapting in some amazing ways.

Now for the tricky part, the analysis of synteny. If you’re not familiar with the concept, you might want to review yesterday’s basic summary of synteny, but it is basically a search for conserved clusters of genes. In this work, they used the logic of synteny to work out the existence of 17 ancestral Chordate Linkage Groups (CLGs). A CLG may roughly compare to a single chromosome in the chordate last common ancestor — it’s a set of genes that are associated with one another in multiple species, and are thought to represent the retention of an ancient organization.

Here’s the wonderfully complicated summary diagram.

i-1a9655c13b7b03cff32e2dfe488f54a3-amph_hum_synteny.jpg
(click for larger image)

Quadruple conserved synteny. Partitioning of the human chromosomes into segments with defined patterns of conserved synteny to amphioxus (B. floridae) scaffolds. Numbers 1-17 at the top represent the 17 reconstructed ancestral chordate linkage groups, and letters a-d represent the four products resulting from two rounds of genome duplication. Coloured bars are segments of the human genome, shown grouped by ancestral linkage group (above), and in context of the human chromosomes (below).

First, along the top they have reconstructed the 17 ancestral CLGs, and they’ve color-coded them: for instance, the genetic contents of CLG #8 (or ancestral chromosome #8, if you’d rather think that way) has been deduced from a comparison of human and amphioxus genomic data, and all those genes have been colored yellow. Below the ancestral CLGs is a diagram of the human chromosome set, from chromosome 1 to 22, with the X chromosome, and homologs to each of the genes in CLG #8 have also been colored yellow. You can see that ancestral chromosome 8 has, over the 500+ million years since, broken up and scattered into human chromosomes 2, 4, 5, 11, 13, and X.

I have to qualify this image a bit, though: don’t get the impression that big chunks of the ancestral chromosomes have survived perfectly intact for half a billion years! What’s illustrated here is a pattern of macro-synteny — what it says is that within a swathe of a particular color, we can find many, but not all genes that can be mapped to a common linkage group. If we did a more fine-grained synteny diagram, where we only mapped continuous blocks of 3 or more genes that were the same, we’d have a much messier, more salt-and-pepper sort of picture.

Within a region of a single color, there has been much scrambling of the local gene order. There have also been additions of individual new genes in either the amphioxus or human genome, and losses of genes. Also, not all genes are included in this summary: approximately 60% of the human genes that have amphioxus orthologs are found in these linkage groups. What each bit of color means is that this is a region that is enriched for a common set of shared genes between amphioxus and human beings, but it has also been leavened with variation and scrambled about internally. What has been preserved is not a literal duplicate of an ancient chromosome, but a segment that retains enough signal above the noise of ages of slow rearrangement that we can detect its affinities.

Still, pretty cool, I think. Evolutionary change hasn’t completely swamped out our origins, only made them fainter and trickier to discern.

There is one other significant detail to this illustration. If you look at the ancestral CLGs, you see that each has more than one colored bar descending from them — there’s four for each. What’s going on here? For each gene (more or less) identified in amphioxus, there tend to be multiple genes in the human. When aligning them, you’ll get multiple roughly equivalent sets of genes lining up with each amphioxus group. What this reveals is that our history is marked by two rounds of whole genome duplications after we branched away from amphioxus. This is also very cool; it might explain some of the greater diversity we see in later chordates, that they have more potential for new combinations and variations of genes.

You might recall that I mentioned that humans and amphioxus have approximately the same number of genes, about 20,000, and be wondering how that jibes with the evidence that there were 2 rounds of duplications. Shouldn’t we have four times as many genes? The answer is no. When a gene is duplicated, more often than not is that one of the copies will accumulate errors and drift away into nonexistence.

Imagine that we have a stretch of chromosome that has these genes on it:

A-B-C-D

A duplication occurs; now we have two regions:

A-B-C-D and A’-B’-C’-D’

Errors take out some of the copies, so we end up with this:

A-.-C-. and .-B’-.-D’

Now, you see, we’ve got a result where the organism hasn’t gained or lost anything overall — it still has an A, B, C, and D gene — we haven’t had a doubling of the total gene numbers, we still have four genes. If we look at the synteny, we’d see one stretch of chromosome, A-.-C-., that lines up with the ancestral A-B-C-D, and we’d also see a second region, .-B’-.-D’, that also lines up with it — there’d be two matches. Even though we haven’t seen a significant net increase in gene numbers, we still have a doubling of the number of syntenic regions.

That’s what this paper is reporting: no major increases in the number of genes, but we are seeing the vestiges of that ancient doubling. Furthermore, the losses aren’t entirely random. There has been a preferential retention of duplicate genes involved in signal transduction, transcriptional regulation, neuronal activity, and developmental processes, exactly what we’d expect to see if new avenues in developmental and behavioral complexity were being explored by our ancestors. So what probably happened is that there was a fairly abrupt duplication event in our history that was largely neutral in its initial effect, and was gradually pared back down, but that some of the duplications generated new capabilities that were promoted by natural selection.

Before our ancestors were even fish, they were Cambrian and pre-Cambrian filter-feeding torpedos, muscular tubes with springy tails that darted through clouds of bacteria and plankton in the seas, harvesting microorganisms in a branchial net, and that probably resembled modern amphioxus more than anything else. That was our primitive niche, motile grazers on suspended particles. Where we vertebrates came from was an accidental set of duplications that created new combinations of genes and new phenotypic variants, some of which had adaptive advantages.

Don’t get too cocky and think that surges in complexity are always a good thing, and lucky for us that we are the outcome. Evolution is blind and sometimes the fortunate result can go the other way: look to the ascidians, which, rather than expanding their genetic library, have been successful by streamlining their genomes, chucking out unnecessary elaborations and juggling a smaller suite of genes around in more dramatic ways. There are many directions evolution can take, and there’s no a priori reason to think our particular path is the most powerful.


Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype.
Nature 453(7198):1064-71.

Comments

  1. #1 sjburnt
    June 26, 2008

    Thank you. I love this stuff!

  2. #2 Jon H
    June 26, 2008

    Looks like an embryonic Mind Flayer.

  3. #3 Becca
    June 26, 2008

    *bursts into song*
    It’s a long way from amphioxus, it’s a long way, to us.
    It’s a long, long way from amphioxus, to the meanest human cuss
    cause it’s goodbye to fins and gillslits, and welcome lungs and hair
    it’s a long long way from amphioxus, but we all came from there

  4. #4 Peter Vaht
    June 26, 2008

    This reminds me of the Pikaia

  5. #5 Glen Davidson
    June 26, 2008

    That’s the thing about evolution. Nearly all of the evidence for it is really based upon the limitations imposed by mutation, duplication, natural selection, etc. So that anyone who accepts the evidence that evolution occurred is implicitly admitting that it occurred by “natural” means.

    All of the synteny is merely due to unfathomable whim, according to ID–that is, if anyone thinks their ideas through.

    Anyhow, I appreciate this info as to its particulars (though I read much of it in Nature already), and the rather amazing conservation of genes and parts of the original organization over more than half a billion years. I simply thought it worth pointing out, yet again, that it has meaning only in theory, while with ID it’s only a swarm of meaningless facts.

    Glen D
    http://tinyurl.com;/2kxyc7

  6. #6 Holbach
    June 26, 2008

    These occasional forays into our natural world you that you offer are beyond my scope of endeavor or expertise, but since they are here and to be known and studied, make evolution a true wonder and a realization that we areso much a part of it. I read this stuff each time you offer it, and though my command of the terminology is limited, it nevertheless fascinates me. Please continue in this regard, as since it is science, it will hold my attention.

  7. #7 Andreas Johansson
    June 26, 2008

    Is it known whether hagfish have the duplications?

  8. #8 Bacopa
    June 26, 2008

    Argh! One of my favorite things to say was that vertabrates can’t have larval forms because we ARE the larval forms. Now I see that may not be true.

    Of course I know that sometimes just hatched fish are called larvae. I see this in my baby White Clouds and cherry barbs if I use a magnifying glass, but White Cloud suckers are still fish. The only maor anatomical revision once they become free swimming is that the mouth moves.

    I’ve had such luck with the cherry barbs I’m thinking about moonshining some GloFish.

  9. #9 ThePetey
    June 26, 2008

    awwww

    widdle itsy bitsy baby cthulhu fetus.

  10. #10 Architeuthis
    June 26, 2008

    Thanks for the supporting article on synteny, that made the genetic switchup a bit easier to follow.

    And excellent point on the a priori pathway evolution takes, it’s hard not to think of evolution as a line to a higher progression of complexity, when species like this thrive on simplicity.
    Cheers.

  11. #11 Architeuthis
    June 26, 2008

    Doh, quick clarification:

    It’s hard not to think of evolution as a line…. but when species like this thrive, it shows that complexity as a trait is not always the best survival mechanism.

  12. #12 Longtime Lurker
    June 26, 2008

    Fun with quote-mining!

    “They… settle down on a solid surface and throw away their… brain and squat permanently as a sessile filter feeder called a” fundamentalist.

    Once again, thanks for bringing the knowledge, PZ!

  13. #13 uncle frogy
    June 26, 2008

    as a relatively new follower/reader of the blog I can see that you are now on “summer break” and to satisfy your “compulsive” need to teach your personal subject you are posting these “lessons” to all to see. I for one am surprised and great full for the effort.
    I personally had to end my formal science education long ago before I could really finish it for a bunch of reasons that were unavoidable at the time I have since at least acquired a tech degree. So I am pleased to read this to me new series of posts. It was biology I was studying long ago and the facts the plants and animals have been my fascination my whole live. The more I learn the deeper my appreciation becomes. I stand in awe to the way things are. thank you though I will have to study the text more before I will be able to really understand and remember it fully. your enthusiasm for and understanding of these details is great to see thanks again. uncle frogy

  14. #14 stanley
    June 26, 2008

    This animal is no more “primitive” than humans are. Evolution is stupid.

  15. #15 PatrickHenry
    June 26, 2008

    Someone has to say it: I ain’t no kin to no amphioxus.

  16. #16 RT NZ
    June 26, 2008

    NO no no no, its a living fossil ,santa , planted it…………suckers

  17. #17 Badjuggler
    June 26, 2008

    I never have to read so many big words when I read about Intelligent Design. My brain hurts.

  18. #18 Metro
    June 26, 2008

    Hey stanley–speak fer yerself, eh?

    It’s not much of a head. The notochord extends all the way to the front of the animal … there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles.

    –Sorry, I thought we were talking about Farfarman for a minute.

  19. #19 Metro
    June 26, 2008

    Hey stanley–speak fer yerself, eh?

    It’s not much of a head. The notochord extends all the way to the front of the animal … there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles.

    –Sorry, I thought we were talking about Farfarman for a minute. He’s busily soiling the thread over at Candid World.

    As for me, what Holbach said goes double. My science education ended somewhere between planaria and my personal discover of human female biology, but you manage to give me handholds to clamber up and at least have a glimpse over the garden wall.

  20. #20 Jason
    June 26, 2008

    Though some of the advanced biology is lost on me, that is a pretty neat creature.

  21. #21 uncle frogy
    June 26, 2008

    dear Stanely:
    come on dear calm down stupid or not evolution describes what we see with in the world our eyes. I am not sure that I understand what you are trying to say.
    do you mean by “primitive” inferior or crude than I would agree. they are highly adapted to the life they lead. evolution has nothing to do with developing “higher forms over lower forms” it is not directed to produce anything specific as can be observed all around us at any time it is not a ladder. I for myself look at it as more of a spreading creating opportunities (space)for other plants and animals and adopting to opportunities and space created by other plants and animals. and yes it is stupid if by that you mean mindless. or is it just you and you just want get off on argument.

  22. #22 Glen Davidson
    June 26, 2008

    Stanley more or less accidentally got to the truth. Evolution is stupid, hence it explains the unintelligent adaptations we see throughout life.

    Intelligence is not stupid, so it does not explain biology.

    Not that Stanley is likely to be intelligent enough to understand how he accidentally told the truth.

    Glen D
    http://tinyurl.com/2kxyc7

  23. #23 SiMPel MYnd
    June 26, 2008

    Are you sure that all those genes for humans weren’t there in the first place and our creator didn’t just “potentiate” them.

    Sorry… I couldn’t resist.

    Great stuff as usual PZ. I particularly liked the synteny discussion yesterday.

  24. #24 Alex
    June 26, 2008

    You made that up. It’s all a fabrication.

    (I love this stuff PZ. You Rock)

  25. #25 Wes
    June 26, 2008

    Wow. I was actually able to follow that and understand it from beginning to end, without getting lost. And I have no training in evo-devo.

    Excellent explanation, PZ, and really fascinating stuff. Thanks for making these kinds of things accessible for us non-scientists. :)

  26. #26 Lee Brimmicombe-Wood
    June 26, 2008

    Stanley more or less accidentally got to the truth.

    Was it accidental? As you rightly say, evolution is not intelligent or guided by intelligence. It is, quite literally, stupid. While rankings of organisms as more or less ‘primitive’ is one of those dangerous notions that leads many laymen astray. I recall SJ Gould warning us against ranking organisms, since evolution might lead in directions other than towards some purported pinnacle.

  27. #27 stogoe
    June 26, 2008

    Fun with quote-mining!

    “They… settle down on a solid surface and throw away their… brain and squat permanently as a sessile filter feeder called a” fundamentalist.

    I seem to remember Dawkins using the same metaphor in Ancestor’s Tale. Probably around the page where our march back through the generations meets up with the urochordates. Except he used ‘tenured professor’ instead of ‘fundamentalist’…

  28. #28 Patricia
    June 26, 2008

    Cool! Looks like something from Farscape.

  29. #29 CJO
    June 26, 2008

    Hey Gordy,

    Learning anything?

  30. #30 Spinoza
    June 26, 2008

    THIS is why I love this site.

  31. #31 Sili
    June 26, 2008

    Errr … I’m pretty sure Stanley meant exactly what you mean – and think that he meant not.

    Why else would he herald the Amphioxus as non-primitive? Wasn’t there a three-post rule in effect at some point?

    Thank you, PZed. So wonderfully clear. And I liked the pretty movie.

  32. #32 Tulse
    June 26, 2008

    I’m sure Schlafly is going to ask for your data, PZ.

    Looks like an embryonic Mind Flayer.

    I got a fireball comin’ online.

  33. #33 SC
    June 26, 2008

    Thanks for this!

    Dear Dr. Putnam:

    I haven’t read your paper, and hardly feel it necessary to do so, but I find your results highly questionable. I demand that you send me all of your data forthwith, and in addition pay my airfare and expenses that I may travel to a tropical island to perform my own research on amphioxus. Otherwise, I shall find it necessary to proclaim the fraudulence of your work in the most public terms. Sincerely,

    SC, Prep School Diploma, B.A., M.A., Ph.D.

  34. #34 SC
    June 26, 2008

    Great minds, Tulse. :)

  35. #35 frog
    June 26, 2008

    Stanley #14: This animal is no more “primitive” than humans are. Evolution is stupid.

    This is one of the cases (which is most) where a word means something different in the technical jargon of a field vs. its common meaning. Primitive here means “more like the original state — less changed”. They have continued to evolve, “as much as” us, but the end result is a less changed ecological niche, and a less changed genome; aka, amphioxus’s history has been more stable than ours.

    It’s got the same meaning in anthropology — when an anthro says the folks in Niugini are primitive relative to us, all they mean is that their lifestyle is more similar to the ancestral state than ours is – not that they’re simpler or “less culturally evolved”, just that their cultural evolution has tended to involve fewer radical shifts.

    This is a constant source of mis-communication. Bias in statistics doesn’t mean the same thing as bias in common language; theory in science doesn’t mean the same thing as theory in common-language; a “consideration of value” is different in law than in standard English.

  36. #36 Steve
    June 26, 2008

    That is so cool. I’ve read that they’re eaten by people and animals in other parts of the world, but they’re only two and a half inches long.

    Such an awesome looking animal.

  37. #37 PatrickHenry
    June 26, 2008

    Re #26 Posted by: Lee Brimmicombe-Wood:

    While rankings of organisms as more or less ‘primitive’ is one of those dangerous notions that leads many laymen astray. I recall SJ Gould warning us against ranking organisms, since evolution might lead in directions other than towards some purported pinnacle.

    I suppose we could refer to “early” and “late” organisms. I’m just groping. PZ probably has the terminology well in hand.

  38. #38 PeteC
    June 26, 2008
    Looks like an embryonic mind flayer.

    I got a fireball comin’ online.

    I don’t, but I am wearing a greased helm of brilliance.

  39. #39 chancelikely
    June 26, 2008

    Bah! Your greased helm of brilliance is no match for my half-githyanki half-gold dragon dire wereskunk archmage/forsaker!

    Thanks for the education, PZ, from this Econ major/incurable D&D nerd.

  40. #40 Louise Van Court
    June 26, 2008

    Interesting write-up. I had to chuckle over this:
    “This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.”

  41. #41 Dave Godfrey
    June 26, 2008

    Well primitive works when used in conjunction with derived. The important thing is not to use the word “advanced” in this context. As Darwin said in his notebooks “Never say higher or lower”.

    Humans are significantly more derived than Amphioxus, which is therefore primitive. I don’t think that Early and Late will work, because organisms (especially parasites) can be secondarily simplified and throw away all sorts of things. Tapeworms and flukes for instance are somewhere (I forget exactly) in the protostomes (complex invertebrates apart from echinoderms, hemichordates, and a few others), rather than down at the base of the animal tree with the acoelmate flatworms where they were traditionally classified.

  42. #42 Matt H
    June 26, 2008

    PZ, you must be brilliant in the classroom….If I’d had a bio teacher/professor like you, I’d probably be in the life sciences instead of math. And thank you for writing these things; this middle-aged technical person is finding his world vastly enhanced by your explanations.

    There was another interesting bit of news in the paper today about an early quadruped fossil – in the same way as the amphioxus, the article said it was unclear where the new fossil sits with respect to the existing record, but it added some new info about how quadrupeds evolved.

  43. #43 Danio
    June 26, 2008

    Wooooh, evolution of the hox gene clusters by tetraeuploidie, didn’t know that.

    hey PZ, it occurs to me that the 8-cell-stage fatemap of amphioxus looks more like the fatemaps of Xenopus and zebrafish than the ascidian fatemap, are there any thoughts on that in the paper? (can’t get that now… registration wall)

    first post!

  44. #44 Danio
    June 26, 2008

    stupid me..

    “are there any thoughts on that in the paper?”

    It wouldn’t be in the same paper, so where is the picture from?

  45. #45 tim Rowledge
    June 26, 2008

    “They… settle down on a solid surface and throw away their… brain and squat permanently as a sessile filter feeder called a”

    I’ll see your ‘fundamentalist’ and raise Dawkins’ tenured professor and point out that that is unpleasantly close to a functional description of 90+% of humans, especially western humans.

    tim. trying not to qualify for the above.

  46. #46 CJO
    June 26, 2008

    especially western humans.
    “Sessile feeders,” perhaps, but, on the evidence, too many eschew the use of a filter.

  47. #47 helioprogenus
    June 26, 2008

    Sometimes it’s great to take a break from hammering at idiotic religious/spiritual people, and actually understand new and novel concepts. The fact that we’re expanding upon our roots, striving for greater and greater understanding, far exceeds the petty imaginary hallucinations that religion has to offer.

    My one question on the earlier post regarding Syntegy was what happens when genes are introduced into our genome since the split with the LCA? How would they be respresented? I guess those segments are the ones in black on that syntegy map. Is that a fair assumption?

  48. #48 Bride of Shrek
    June 26, 2008

    “It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.”

    ..presumably without the loud shirts though.

  49. #49 Uncephalized
    June 26, 2008

    I love this stuff. I don’t always understand the terminology, but it grabs my interest and holds it until the last word. It’s so fascinating to see where we come from and the millions of other paths life has taken since we diverged from our cousins. Plus all these weird sea creatures are great fodder for monster ideas when I write stories.

  50. #50 David Marjanovi?, OM
    June 26, 2008

    Of course I know that sometimes just hatched fish are called larvae.

    What would you call a tadpole?

    There was another interesting bit of news in the paper today about an early quadruped fossil – in the same way as the amphioxus, the article said it was unclear where the new fossil sits with respect to the existing record, but it added some new info about how quadrupeds evolved.

    The phylogenetic position of Ventastega (which is in today’s Nature rather than in last week’s) is very clear, see below; what isn’t clear is whether V. had fingers & toes and/or fin rays on its extremities, because the extremities haven’t been found yet. There’s just the skull & lower jaw, the shoulder girdle, the ilium (part of the hip girdle), possibly a rib, and possibly a fin ray of the tail fin.

    --+--Eusthenopteron (f)
      `--+--Panderichthys (f)
         `--+--Elpistostege
            |--Tiktaalik (f; d?)
            |--Elginerpeton
            `--+--Ventastega
               `--+--Acanthostega (d)
                  `--+--Metaxygnathus
                     `--+--MGUH VP 6088
                        |--Ichthyostega (d)
                        |--Densignathus
                        `--+--Whatcheeria
                           `--+--Pederpes (d)
                              `--+--Greererpeton (d)
                                 `--+--Crassigyrinus (d)
                                    `--+--Baphetes
                                       `--+--Balanerpeton (d)
                                          |--Dendrerpeton (d)
                                          `--+--Silvanerpeton (d)
                                             `--+--Proterogyrinus (d)
                                                `--Eoherpeton (d)
    

    This is a strict consensus of 64 equally most parsimonious trees; this is where the divergences into more than two branches come from — they represent uncertainties. (f) means fin rays are known, (d) means digits are known; Tiktaalik has fin rays and has what may or may not be homologous digits. MGUH VP 6088 is the specimen number of a new animal from Greenland that isn’t yet described. Balanerpeton and Dendrerpeton are temnospondyls, so they would most likely have been found as sister-groups if more characters had been included, which wasn’t done because they aren’t the focus of this analysis; together they are most likely our closest relatives in this tree. Proterogyrinus and Eoherpeton are anthracosaurs.

  51. #51 Fernando Magyar
    June 26, 2008

    PZ, when the heck is your book coming out? If your taking credit cards I’ll pre order now. Oh, and what’s with acsidians accumulating vanadium starting in embryogenesis?

  52. #52 pcarini
    June 26, 2008

    there isn’t even a face, just an open hole fringed with tentacles.

    I misread that on the first skim through, and now I have a new favorite insult!

    Excellent writeup as always PZ.

  53. #53 Fernando Magyar
    June 26, 2008

    You’re not “your” Argh #$@^%%!

  54. #54 Fernando Magyar
    June 26, 2008

    Shit! never mind, I’ve had a very long day. Sheepish grin.

  55. #55 Holbach
    June 26, 2008

    David Marjanovic @ 50 I am truly awed with incomprehension, but still awed nevertheless! Science may at times be beyond the reach of the non-specialist, but it is still there to marvel for it’s application to all that we know, and immaterial to the minds that don’t wish to know.

  56. #56 Dave Godfrey
    June 26, 2008

    Have you got any more information about the putative digit in Tiktaalik? I don’t recall anything being mentioned at the time.

  57. #57 Pandragon
    June 26, 2008
    It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

    ..presumably without the loud shirts though.

    That’s the tunicates department. :D

  58. #58 Holbach
    June 26, 2008

    Bride of Shrek @ 48 “Presumably without the loud shits though(or was it shirts?)” If you want a peaceful spot on the beach, it is a lot easier to close your eyes than to stuff your ears, depending of course, on the offending shits or shirts.

  59. #59 Christopher Petroni
    June 26, 2008

    I can’t believe no one else has commented on this!

    It’s a long way from amphioxus, it’s a long way, to us.
    It’s a long, long way from amphioxus, to the meanest human cuss
    cause it’s goodbye to fins and gillslits, and welcome lungs and hair
    it’s a long long way from amphioxus, but we all came from there

    That was freaking brilliant, and you are my new favorite human being, Becca.

    I actually sang it to myself!

  60. #60 stan-the-man
    June 26, 2008

    anyone show me a mutation that creates a gill from a non-gill? Heck, or show me any mutation that adds a new structure (or part of a structure.)

  61. #61 stanley
    June 26, 2008

    Evolution is indeed stupid. All you people are suckers for storytellers like PZ.

  62. #62 Pandragon
    June 26, 2008

    @54: It’s been around for decades.

    It’s a Long Way From Amphioxus

    A fishlike thing appeared among the annelids one day
    It hadn’t any parapods or setae to display
    It hadn’t any eyes or jaws or ventral nervous chord
    But it had a lot of gillslits and it had a notochord.

    Cho.
    It’s a long way from amphioxus
    It’s a long way to us.
    It’s a long way from amphioxus
    To the meanest human cuss.
    So goodbye to fins and gillslits
    Hello lungs and hair,
    It’s a long, long way from amphioxus
    But we all came from there.

    Well, it wasn’t much to look at and it scarce knew how to swim
    And Nerius was very sure it hadn’t come from him.
    The mollusks wouldn’t own it and the arthropods got sore
    So the poor thing had to burrow in the sand along the shore.

    Cho.

    It burrowed in the sand before it grabbed in with its tail
    And said gillslits and myotomes are all to no avail.
    I’ve grown some metapleural folds and sport an oral hood
    But all these fine new characters don’t do me any good.

    Cho.

    He soaked a while down in the sand without a bit of pep
    Then he stiffened up his notochord and said: “I’ll beat ‘em yet.”
    They laugh and show their ignorance, but I don’t mind their jeers
    Just wait until they see me in a hundred million years.

    Cho.

    My notochord will stiffen to a chain of vertebrae
    As fins, my metapleural folds will agitate the sea
    My tiny dorsal nervous chord will be a mighty brain
    And vertebrates will dominate the animal domain.

    Cho.

  63. #63 Pandragon
    June 26, 2008

    Previous post should have been directed to #59.

  64. #64 Charlie Foxtrot
    June 26, 2008

    Well, I’m an IT nerd – but even I managed to follow most of that, and it is fascinating!
    This is such a great blog!
    “Pharyngula – come to kick the Fundies in the balls, stay for the Science!”

  65. #65 Charlie Foxtrot
    June 26, 2008

    @ ‘stanley’ – If you’re really interested, there’s a whole world of textbooks out there. Reject the ignorance and get reading.
    In my short time here I have seen that genuine questions are welcome here, indignant demands are not.
    Go find some questions.

  66. #66 Holbach
    June 26, 2008

    Stanley @ 61 and possibly @ 60? No, what you meant to say is that all religionists are insane moronic cretins who believed that their shit imaginary god breathed life into them from massive rectums in the cesspit of dementia, and who are not worth the shit they were born from. Now you can call your ghost god down from wherever it isn’t and lay waste to this site that treats your kind as the deranged product of religious insanity. Come on, let’s see this imaginary shit god of yours, you slime mold cretin!

  67. #67 Geoff
    June 26, 2008

    Fascinating. Are they any good to eat?

  68. #68 pcarini
    June 26, 2008

    …who believed that their shit imaginary god breathed life into them from massive rectums…

    Perhaps that’s a little garbled and the god breathed life into their rectums, those being the first available chance. (“In the beginning, there was an asshole…”)

  69. #69 Pierce R. Butler
    June 26, 2008

    Damn – all this science stuff.

    I came here because this blog has a reputation for verbal violence against faith and the faithful, and instead there’s all this biology and explanations and guided tours through the labs.

    Not even any dancing dodos, dammit.

    I’m gonna go tell everybody that PZ’s reputation is a fraud, and nobody should ever come here any more again!

  70. #70 amphiox
    June 26, 2008

    A whole genome duplication would most certainly be a fatal mutation for the majority (all?) of modern vertebrates. Clearly at more than one point in the history of our lineage, genome duplications were neutral mutations. Does anyone know if a whole genome duplication is a neutral or non-neutral mutation for a modern amphioxus?

  71. #71 Kseniya
    June 26, 2008

    I love how the people who believe that God breathed life into dust are the same ones who call the theory of evolution “a fairy tale”. It’s all bullshit; anyone with half a brain knows it was Prometheus messin’ with his Play-Do.

  72. #72 pcarini
    June 26, 2008

    It’s all bullshit; anyone with half a brain knows it was Prometheus messin’ with his Play-Do.

    Oh damn, they must’ve totally screwed up that story when I heard it in school…

  73. #73 stanopoly
    June 26, 2008

    any answer to #60 you evo losers?

  74. #74 Kseniya
    June 26, 2008

    Fuck off, ignorant fool.

    Oh. I’m sorry. I meant to say, “Those answers are available to those who truly wish to learn.”

    Unfortunately, you’re obviously an anvil troll, therefore you will not seek, because you do not wish to learn.

    Enjoy your Dark Age.

  75. #75 bybelknap, FCD
    June 27, 2008

    All you people are suckers for storytellers like PZ.

    Yeah, because goddidit is a much better explanation for the diversity of life than evolution, you ass-hat.

    If you (Stan%whatev) weren’t suffering from such a severe case of cephalo-caudal inversion you might have a chance to understand. But your head is so far up your own ass your burps smell like farts. Or something.

    So I’ll add my “fuck off, ignorant fool.” to Kseniya’s.

  76. #76 stanstrum
    June 27, 2008

    Kseniya, you poor miserable fool…why don’t you stop running your mouth and answer my challenge.

  77. #77 Ichthyic
    June 27, 2008

    Kseniya, you poor miserable fool…

    this has GOT to be parody.

  78. #78 Wowbagger
    June 27, 2008

    Kseniya wrote:

    anyone with half a brain knows it was Prometheus messin’ with his Play-Do.

    Oh, I love that. From now on I will describe all creotard fundies as Skydaddy’s Special Magical Play-Do Men?.

    As for you stan(insert suffix here) – here’s a hint: the posters won’t bother to answer inane questions unless you do some reading first. I suggest you spend a couple of hours on Talk Origins.

  79. #79 stansmith
    June 27, 2008

    So don’t you evos feel pretty stupid that of all the trillions of bodily structures in the universe that you cannot account for the arrival of even one of them via your theory (RMNS)? I mean you must feel like complete fools who’ve fallen hook, line and sinker for the fairytales told by the likes of storytellers such as PZ Nose-Miner! If you doubt this, prove me wrong; show me the scientific verfication of the addition of a new bodily structure via random mutation.

  80. #80 stan
    June 27, 2008

    you bunch of wackjobs.

  81. #81 Wowbagger
    June 27, 2008

    Stan, are you suffering from multiple personality disorder? Seriously, seek some help. With your faith being as strong as it is, though, I don’t imagine you’d want to trust in medicine, it being one of teh evil sciences that are making baby jesus cry.

    Go find yourself some strong oil, annoint yourself up real nice, pray really hard and see what happens.

  82. #82 Kseniya
    June 27, 2008

    Stan, – do you have even the remotest trace of a whisp of a ghost of a foggy clue? Don’t you realize what you are?

    Let me tell you: You’re one in a long series of ignorant, arrogant fools.

    I have a few questions for YOU: Why should anyone here answer your question? Are you looking for a nurse-maid? Are you genuinely looking for answers? Did it ever – once, just once – occur to you to ask without being an asshole about it? No, of course not – you can’t change what you ARE, can you.

    I also have a question for everyone else: Would you describe Stan as irritating, or merely boring? Hmm… I sense a poll coming on.

  83. #83 stanlin
    June 27, 2008

    tapping tapping….sighing…waiting…….dang you people are pathetic….answer my dang challenge you little twerps. Stick up for this pig you call science.

  84. #84 Ichthyic
    June 27, 2008

    Are you genuinely looking for answers?

    oh come on!

    what do you think?

  85. #85 Wowbagger
    June 27, 2008

    Stan,

    I’m not a scientist, dickhead. I don’t have to tell you squat that you can’t find out for yourself by doing some research.

    Take your questions and shove them up your jesus-hole.

  86. #86 stan
    June 27, 2008

    geez, wowbagger, and where would be a good place for finding mutations that add new structures? You think, since you brought it up, that you can muster up the name of a website, you little know-nothing punk?

  87. #87 stan
    June 27, 2008

    And you freaks never did show me scientific validation of natural selection creating genetic fitness within a population. Got that, homos?

  88. #88 Wowbagger
    June 27, 2008

    Stan…are you…coming on to me?

  89. #89 Bride of Shrek
    June 27, 2008

    Stan hearts Wowbagger!!!

    Wowbagger, you lucky thing you.

  90. #90 stan
    June 27, 2008

    no, Wow…it’s not a come-on…….it’s actually a push-off….and I’m tired of this joint, so I’ll be leaving now…..this place is good for nothing but watching evos waste time talking about lies, fibs and fairytales. Good luck with all that, suckers.

  91. #91 Kseniya
    June 27, 2008

    You don’t deserve our help, you rabid, mange-eaten gutter-cur. It’s clear you don’t want to know. If you did, and took five minutes to actually look, you’d find multiple references to experimental “validation of natural selection creating genetic fitness within a population” right here on this blog, all within the past week.

  92. #92 Wowbagger
    June 27, 2008

    No, Stan, don’t go!

    Sigh. This always happens. I get the chance to be the secret gay love-slave of a closeted, hate-filled fundy and it all falls apart.

    Seriously, Stan, if you’re even vaguely serious you should come back at a more reasonable hour when more people are online. Then you might get the serious thrashing answers you’re after.

  93. #93 Nerdette
    June 27, 2008

    We sang “It’s A Long Way From Amphioxus” in my Invert Bio class. Our amphioxius in lab was a sad little guy, but it was fascinating watching it burrow under the sand.

    And to add to the creationist bashing, Stan, please teabag a blender. Thank you.

  94. #94 Tulse
    June 27, 2008

    Stick up for this pig you call science.

    I’m perpetually amazed that people can post statements like this on the frickin’ Internet completely unironically.

    Yeah, there was no science at all involved in developing a system that allows you to display your ignorance to potentially millions of people around the planet, nosiree.

    I think creationists should be forbidden from using any technology that isn’t mentioned in the Bible. (You’ll notice we never have to tangle with any Amish here…)

  95. #95 Jeremy
    June 27, 2008

    Where is the endostyle on the pictures of the Lancelet? There are 5 important features of a chordates right?

  96. #96 Jeremy
    June 27, 2008

    “anyone show me a mutation that creates a gill from a non-gill? Heck, or show me any mutation that adds a new structure (or part of a structure.)” – Stan-The-Man

    Evolution has nothing to do with “mutations” in the Hollywood monoster sense of the word. Evolution is more about the fact that you’re probably a different height to both your parents. The majority of significant mutations that you see are caused by external factors; chemicals etc. These aren’t the cause of evolution. It’s the differences between healthy parents and their healthy children that drives evolution.

    The evolution of gills is pretty straight forward (at least from a simple perspective). All gills really are is lots of very small blood vessels (capillaries) running very close to the skin so that gasses in the water can pass into the blood. We can clearly see that as animals increase their metabolism they increase their need for oxygen and to do this they increase the surface area of their gills (or lungs). For the sake of practicality, they do this by developing the complex structures we see in fish (as well as gill arches, operculums etc.)

    The things needed to evolve gills is really just skin and blood (or at least some kind of internal liquid). We can see these features in pretty much all animals, and of course, we can see the remains of gills in reptiles, birds and mammals.

    While I understand that we can never understand the actions of God, it is fascinating that she designed humans with gills that we never use and only appear in our early development.

  97. #97 Mystyk
    June 27, 2008

    “There are many directions evolution can take, and there’s no a priori reason to think our particular path is the most powerful.”

    Beautifully said.

  98. #98 Nick Gotts
    June 27, 2008

    Someone has to say it: I ain’t no kin to no amphioxus.
    – Patrick Henry

    Some amphioxus has to say it: I ain’t no kin to no IDiot.

  99. #99 dinkum
    June 27, 2008

    Jeremy (#98), that was a noble effort, but the Stanster is appearing here merely as a demonstration of the sometimes deleterious effects of inbreeding.

  100. #100 dinkum
    June 27, 2008

    Whoops, make that #96.
    More coffee…

  101. #101 Fernando Magyar
    June 27, 2008

    Stanlin re #3,

    Disclaimer, I’m not a biologist though I did take graduate level courses in subjects such as zoology, cytology, physiology, biochemistry and genetics etc. However as layman I can tell you that anyone with a little bit of serious effort can find the knowledge you claim to seek. It really isn’t that hard to understand the concepts. Here is an example of the kind of information that is available for anyone to look at.

    http://www.ncbi.nlm.nih.gov/pubmed/10226012

    Developmental expression of Pax1/9 genes in urochordate and hemichordate gills: insight into function and evolution of the pharyngeal epithelium.

    Yes, one has to do some ground work to be able to understand the language and you can’t expect others to do that for you.
    So if I might make a suggestion, not that I have any expectation that you will do so, go educate yourself.
    Oh, and while imaginary friends may play an important role in a child’s development most children eventually get past that phase and grow up. When you do the same come back and have a conversation and try to ask your questions again. For now you need to be put in your room for a time out.

  102. #102 Fernando Magyar
    June 27, 2008

    Yeah bring on the coffee that was stanlin@ 83

  103. #103 Rrr
    June 27, 2008

    Thanks for posting this, PZ. Reading your wonderfully worded science posts is always a delight.

  104. #104 Torbjörn Larsson, OM
    June 27, 2008
  105. #105 David Marjanovi?, OM
    June 27, 2008

    David Marjanovic @ 50 I am truly awed with incomprehension, but still awed nevertheless!

    Please do ask questions when you have some. Temnospondyls are this kind of beast, anthracosaurs that one including that one. And don’t be awed at me, I just parroted the paper…

    —————

    Have you got any more information about the putative digit in Tiktaalik? I don’t recall anything being mentioned at the time.

    The bones near the ends of its paired fins are suggested, in the paper that describes Tiktaalik, to be homologous to digits. The branching pattern in which they are arranged is, however, different from the branching pattern in which digits are usually thought to be arranged. We need yet more fossils and yet more development genetics…

    ——————

    anyone show me a mutation that creates a gill from a non-gill?

    Gills are little more than outgrowths of the gill slit walls. Express the gene called shh in the wrong place — one mutation! –, and something will sprout. If it’s well vascularized, it can’t help functioning as a gill.

    ——————–

    A fishlike thing appeared among the annelids one day

    Man, must that be old. Chordates and annelids haven’t been considered close relatives for many decades.

    The annelid with the garbled name is Nereis.

    —————–

    A whole genome duplication would most certainly be a fatal mutation for the majority (all?) of modern vertebrates.

    Why? It happens every once in a while. Off the top of my head, there’s a tetraploid rodent species in South America, AFAIK closely related to the chinchilla. It’s nowhere near as common as in flowering plants, but it does occur.

    ————-

    Where is the endostyle on the pictures of the Lancelet?

    It’s there, but it isn’t dyed.

    There are 5 important features of a chordates right?

    There is no such thing as “important”.

    ——————-

    While I understand that we can never understand the actions of God, it is fascinating that she designed humans with gills that we never use and only appear in our early development.

    No, we never have gills. We have gill slits, gill arches and all the rest of the architecture (except the gill lid), but we no longer switch gill growth on.

  106. #106 David Marjanovi?, OM
    June 27, 2008

    (Wow, I wrote a comment with three links, and it immediately got through… great!)

  107. #107 doug livesey
    June 27, 2008

    Becca — loved the song!
    Doug. x

  108. #108 stanner
    June 27, 2008

    Wow: “Sigh. This always happens. I get the chance to be the secret gay love-slave of a closeted, hate-filled fundy and it all falls apart.

    Seriously, Stan, if you’re even vaguely serious you should come back at a more reasonable hour when more people are online. Then you might get the serious thrashing answers you’re after”

    Ok…I’m here and waiting. While I was gone, someone said they have proof of natural selection creating genetic fitness in a population…another guy said mutations aren’t important to evolution…another guy claimed the ancient re-expression of the pax9 gene equated to a scientifically-verified mutation. This crap is just delicious. Bring on some more…I’m hungry.

  109. #109 extatyzoma
    June 27, 2008

    creation could be true if biologists found that the hereditary molecules of organisms shared no specific similarities whatsoever (as you would predict if evo were true) so a dogs DNA would be no more similar to that of a dandelions as it was to a wolfs.

    An all powerful magical creator surely wouldnt even need a common genetic alphabet, in fact why would it need any physical mechanism for organismic identity at all. If orgs contained no heritable information then the case for a creator would be more plausible, as it stands though biology shows quite, quite the opposite, nicely demonstrated in this article. great stuff!!

  110. #110 s1mplex
    June 27, 2008

    It’s been a while since I’ve been able to even hear the word gills, without immediately thinking of one of my all-time favorite pharyngula posts:

    http://scienceblogs.com/pharyngula/2006/06/deep_homologies_in_the_pharyng.php

    Absolutely fascinating, and always good for a re-read.

  111. #111 extatyzoma
    June 27, 2008

    “there isn’t even a face, just an open hole fringed with tentacles.”

    source: H.P Lovecraft. unpublished diary secretly held in a big museum.

  112. #112 dinkum
    June 27, 2008

    “Evolution has nothing to do with “mutations” in the Hollywood monster sense of the word.”

    “…another guy said mutations aren’t important to evolution…”

    Yeah, that’s exactly what he said. Whatever.

  113. #113 Fernando Magyar
    June 27, 2008

    another guy claimed the ancient re-expression of the pax9 gene equated to a scientifically-verified mutation.

    Really? That’s a bit of a surprise to me, where exactly did I say that?

  114. #114 Kseniya
    June 27, 2008

    While I was gone, someone said they have proof of natural selection creating genetic fitness in a population…

    Start here: http://myxo.css.msu.edu/ecoli/

    Check references here.

    “another guy said mutations aren’t important to evolution…”

    Who said that? Where? Are you really that dense? No, surely not – you’re badly misrepresenting something. Intentionally. Ass.

    another guy claimed the ancient re-expression of the pax9 gene equated to a scientifically-verified mutation

    Yes, and provided a link, which was more than you deserve. You continue to demonstrate your rank dishonesty. Will you ever get tired of playing the role of idiot punk? Please say yes. Please.

  115. #115 RAM
    June 27, 2008

    Thank you PZ!
    I love your site for this type of info……

  116. #116 bybelknap, FCD
    June 27, 2008

    Hey, stantard, you said you were leaving. Liar. You are yet another liar for jesus. Fuck you and your lies, stantard.
    You are also lazy. A lazy, lying jesus tard. Shut your fucking face, uncle fucker, until you make the effort to educate yourself. Better yet, just eat a lump of cold poison and die already. You are useless. I only hope you haven’t had the opportunity to breed and add another dose of willful ignorance to the world. You deserve nothing better than to live in a shit-hole without the benefit of electricity or clean water. Better yet, just kill yourself. Stop wasting valuable oxygen you demented fucktard. Get one of your ignorant creotard buddies to nail you up to a cross – who knows? If you love jesus enough maybe you’ll come back to life. That’s an empirical test I’d like to see.

  117. #117 Kseniya
    June 27, 2008

    Having a bad day, Bybel? :-p

  118. #118 Libby
    June 27, 2008

    Hehe! My teenager still remembers me singing the Amphioxus song to him when he was tiny. :)

  119. #119 Metro
    June 27, 2008

    Hey Stan(jective): Yuh came back! I thought you said you were coming off or something …

    On observation: “…..this place is good for nothing but watching evos waste time talking about lies, fibs and fairytales.”

    If you actually DO leave, ever, then we can stop discussing religion and get back to the science … which is fascinating. Have you ever read any? I’m only a layperson myself (often as possible) but PZ makes this stuff quite accessible.

    And I think you’re being quite cruel, teasing poor Wowbagger like that.

  120. #120 Jon H
    June 27, 2008

    It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

    Order your DVDs from Amphioxus Gone Wild! Now!

    Here’s a sample…

    “Hey, you’re really pretty. How about you put on this dye and let us take pictures of your hidden structures?”

  121. #121 Longtime Lurker
    June 27, 2008

    You know the trolls have gone drastically downhill when you start to miss Walton.

    Not that I miss Walton…

  122. #122 raven
    June 27, 2008

    stan the future mall shooter:

    you bunch of wackjobs.

    Weren’t you the troll who was threatening to shoot up a mall or something a while back? Hasn’t happened yet. Never believe a creo moron, they lie about everything.

    Stan you are one in an endless series of mentally ill creos. Try to be more original and interesting. Insults are so 2007 these days. It is easy. Why don’t you describe your diagnosis, most pointless arrests for stupid stuff, and the medications you are supposed to take but never do.

    For extra credit, what are the voices in your head saying now? Probably complaining that you can’t follow directions from god very well.

  123. #123 Sili
    June 27, 2008

    Oh dear.

    My apologies for defending Stan* upthread. I obviously need to be more jaded.

  124. #124 prof weird
    June 27, 2008

    stan the blithering gibbertwit doth vomit forth :

    So don’t you evos feel pretty stupid that of all the trillions of bodily structures in the universe that you cannot account for the arrival of even one of them via your theory (RMNS)?

    TRILLIONS of structures ? Please show your math, twit.

    Do you know of some bodily structures on organisms on a planet in the Tau Ceti system that no one else knows about ?

    To date, all bodily structures are explainable via mutation/selection.

    Unless one has shoved his head three feet up his own arse, and actually EXPECTS new parts to just ‘POOF !!!!’ onto organisms from nowhere.

    And your ‘explanation’ is what ? An unknowable being somehow did something sometime in the past for some reason ?

    I mean you must feel like complete fools who’ve fallen hook, line and sinker for the fairytales told by the likes of storytellers such as PZ Nose-Miner!

    Nope – we’ve examined REAL WORLD DATA, which so far supports evolution. That you wish to remain mired in the willful stupidity and gibbering inanity of Magical Skymanism is hardly anyone’s fault but your own.

    REAL science and evolution don’t have fairytales – that sort of nonsense is left to IDiots, creationuts, and theoloons.

    Again, your ‘explanation’ of the data is what again ?

    And just why does ‘GODDIDIT !!!!!’ NOT qualify as a fairytale ?

    If you doubt this, prove me wrong; show me the scientific verfication of the addition of a new bodily structure via random mutation.

    http://scienceblogs.com/pharyngula/2007/03/evolution_of_the_jaw.php

    http://scienceblogs.com/pharyngula/2007/01/evolution_of_the_mammalian_vag.php

    http://scienceblogs.com/pharyngula/2006/07/flap_those_gills_and_fly.php

    “Regulating Evolution”, Sean B Carroll, B Prud’homme, N Gompel, Scientific American May 2008, pg 61+ : whether sticklebacks have pelvic spines or not is regulated by the Pitx1 gene.

    “The ORIGIN of the parathyroid gland”, Okabe M, Graham A, Proceedings of the National Academy of Sciences 101 (51): 17716-19, Dec 2004

    (You may now being frantically waving your arms, stomping your foot, and bellowing insults in a feeble attempt to evade the fact that you’ve been shown to be wrong.

    Or start dragging the goalposts backward and translight speed, as is common with your ilk.)

  125. #125 amphiox
    June 27, 2008

    David Marjanovi?, thanks. A tetraploid rodent is fascinating. Until now I had assumed that since most triploidy mutations lead to spontaneous abortions, a whole genome duplication would be that much worse, and was under the impression that there was something special about vertebrate gene regulation that made too many excess gene copies detrimental to development, unlike in plants.

  126. #126 Danio
    June 27, 2008

    Xenopus laevis (the model organism!) is also tetraploid,
    which means its use as a model organism is limited, because it’s hard to get homozygous mutants. You have to cross 4 same allels in it instead of 2.

    http://en.wikipedia.org/wiki/Xenopus_laevis

  127. #127 MTran
    June 27, 2008

    I think I saw some stannoid commentary a while back on a football site during the playoffs.

    The guy there was claiming that football is not actually a ball “game” because it has neither bats nor bases, which, at best, indicates a possible loss of game information. Plus, everyone knows that balls are spherical, so it is neither a game nor does it have any balls.

  128. #128 Wowbagger
    June 27, 2008

    Stan, you came back! Does that mean you do love me?

    Like I said, if you come back at an hour when some of the regular posters are online, you’d get exactly what you were looking for – in this case all the evidence and explanations you need. Plus the sound thrashing that you seem to desire – though i can’t imagine the Pharyngula crowd are enjoying it too much; it’s like watching a bear savage a caterpillar.

    But that isn’t enough, is it? You’ll just keep finding more gaps to cram your ever-diminishing god into while proudly lying for jesus about what it all means.

    Begone, asshat.

  129. #129 stanley
    June 27, 2008

    professor weird: “To date, all bodily structures are explainable via mutation/selection.”

    screw explanations…heck, I could say the same thing: “To date all bodily structures are explanable by a mind (of God or otherwise).

    But please show me your stupid science…show me a scientifically-verified random mutation that adds a new bodily structure or a new part of a bodily structure.

  130. #130 raven
    June 27, 2008

    stan the crazy future mall shooter:

    show me a scientifically-verified random mutation that adds a new bodily structure or a new part of a bodily structure.

    WHAT IS POLYDACTYLY?

    Polydactyly, or extra digits, is a common trait among cats, particularly it seems, among Celtic cats and cats on part of America’s Eastern coast and South West Britain. This distribution may well be linked. Except for Twisty Cats, polydactyly is not a product of bad breeding. It is simply a naturally occurring genetic variation and, as noted later on, polydactyly is found in fossil reptiles – meaning that five digits might be the abnormal form! Only one form of polydactyly is known to be harmful.

    Why bother. You will just Move The Goal Posts. Creos don’t have enough imagination to even be interesting and crazy, just crazy. So Stan, which mall will you attack? Are you going to take drugs and drink beforehand?

    For anyone not familiar with stan, he is crazy, drunk a lot, and has been known to make some ugly threats involving violent death to other people.

  131. #131 David Marjanovi?, OM
    June 27, 2008

    I had assumed that since most triploidy mutations lead to spontaneous abortions, a whole genome duplication would be that much worse

    No, because mitosis is much easier for tetraploid cells than for triploid ones.

    (And I really should have remembered the common lab frog.)

  132. #132 Wowbagger
    June 27, 2008

    For anyone not familiar with stan, he is crazy, drunk a lot, and has been known to make some ugly threats involving violent death to other people.

    And he’s fabulously homophobic – we all know that that means, don’t we?

    Unfortunately, Stan, science can’t randomly mutate you a functioning brain. Try praying instead.

  133. #133 raven
    June 27, 2008

    Polydactyly itself is also known as hyperdactyly or supernumary digits and occurs in many animals (including humans) as a spontaneous mutation or hereditary trait. The mode of inheritance – dominant or recessive – varies between species. Instances and illustrations of human polydactyly (for comparison purposes) are given at the end of this article.

    There is also a mutation in chickens that makes them grow teeth and mutations in humans that cause them to grow fur all over and another that results in tailed people.

  134. #134 stanzer
    June 27, 2008

    polydactyl is just a duplication of what was already there. Nothing new. Anyone else?

  135. #135 Wowbagger
    June 27, 2008

    An opposable thumb is basically ‘another’ finger, Stan – you don’t think that having that counts as a ‘beneficial mutation’?

    Surely you can’t be that obtuse.

  136. #136 Longtime Lurker
    June 27, 2008

    Stan, they did something to you at that “Love in Action” camp. Why not embrace the real you? You see, your amorous feelings have not been considered a mental illness for a couple of decades, but your “mall shooter” tendencies are another thing altogether.

  137. #137 Dave Godfrey
    June 27, 2008

    Stan, in segmented animals duplication is tremendously important, because once a a structure is duplicated there are two structures performing the same function and one can diverge into another role.

    This is incredibly common with genes. For instance there is a large family of genes producing several haemoglobins, they are closely related to the myoglobin family of genes, and shared a common ancestor.

    Duplication of a structure or a gene allows divergence and then you start getting new structures. You won’t see something new immediately. Which is exactly what evolution predicts- gradual modification of existing traits.

  138. #138 raven
    June 27, 2008

    stan the mall shooter wannabe:

    show me a scientifically-verified random mutation that adds a new bodily structure or a new part of a bodily structure.

    raven predicting stan’s mental slowness:

    Why bother. You will just Move The Goal Posts. Creos don’t have enough imagination to even be interesting and crazy, just crazy.

    Scientists have discovered that rarest of things: a chicken with teeth – crocodile teeth to be precise.

    Contrary to the well-known phrase, ‘As rare as hens’ teeth,’ the researchers say they have found a naturally occurring mutant chicken called Talpid that has a complete set of ivories.

    The team, based at the Universities of Manchester and Wisconsin, have also managed to induce teeth growth in normal chickens – activating genes that have lain dormant for 80 million years.

    So predictable. You asked for a mutation that produces “a new part of a bodily structure.” Extra toes are certainly new parts. You also ignored my other three examples, teeth in chicken, furry humans and tailed humans.

    As usual stan will Move The Goal Posts again. Or get drunk and threaten to kill people again. He isn’t bright enough to even come up with his own excuses or craziness.

    This is why the creos will lose. They have lost in the domains of educated people and science a century ago. All that thye have left are Death Cultist fanatics with mental illness, no education, and low IQs. Like stan.

  139. #139 Charlie Foxtrot
    June 28, 2008

    For anyone not familiar with stan, he is crazy, drunk a lot, and has been known to make some ugly threats involving violent death to other people.

    And he’s fabulously homophobic – we all know that that means, don’t we?

    He’s a Republican senator???

  140. #140 bybelknap, FCD
    June 28, 2008

    stanshitbag doesn’t deserve the good information you fine ladies and gents are giving to him. He deserves shackles and bread and water in an underground cell. And lots of insults. More insults than at which a stick can be shookended.

  141. #141 bybelknap, FCD
    June 28, 2008

    @ Kseniya,
    Nope, I just enjoy a good verbal evisceration along with my church burnin and baby eatin.

  142. #142 Torbjörn Larsson, OM
    June 28, 2008

    I could say the same thing: “To date all bodily structures are explanable by a mind

    Wouldn’t mean a thing since you don’t have a theory predicting it. You can’t even argue that it would happen randomly (and if you did it would be highly improbable as opposed to the results of the mechanisms of evolution).

    And if you pulled your thumb out from your ass and actually made a testable theory which predicts exactly what evolution does, it would be noncompetitive as it would have an unspecified amount of unobservable agents involved instead of being based on observed mechanisms. Agents that further need an explanation of exactly the kind that such a theory aimed to solve, i.e. it is a circular argument.

    Most charitably it is a mindless argument.

  143. #143 Silvia
    January 15, 2009

    great great blog. Too bad PZ is an atheist. i respect it :)
    “Science without religion is lame, religion without science is blind.” (Albert Einstein)

  144. #144 cet
    March 26, 2009

    thanks. by Brooklyn

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