It’s a shame I have to say that right from the beginning.
I’m beginning to develop a distaste for computer models of biological processes, which is a shame. From Andrulis to Fleury to Pivar, the field is tainted with people who don’t know a lick of biology but are good at inventing algorithms that go spinning off into never-never land, spawning odd and suggestive shapes that, in their happy ignorance, they assign to real organisms.
The latest is a guy named Eric Werner who, in a surprising change of pace, has a model that does not involve whorls, spirals, vortices, or toroids, the usual objects of crackpot obsessions, and is instead about inversions. He has a model for the production of skeletons, which is his, and which explains both exoskeletons and endoskeletons. “Exo”, “endo”, get it? All you have to do to turn one into the other is to turn the animal inside out.
That’s the other thing about these kinds of modelers — it’s got to be a really simple transformation that does the job all in one step.
An intriguing unanswered question about the evolution of bilateral animals with internal skeletons is how an internal skeleton evolved in the first place. Computational modeling of the development of bilateral symmetric organisms suggests an answer to this question. Our hypothesis is that an internal skeleton may have evolved from a bilaterally symmetric ancestor with an external skeleton. By growing the organism inside-out an external skeleton becomes an internal skeleton. Our hypothesis is supported by a computational theory of bilateral symmetry that allows us to model and simulate this process. Inside-out development is achieved by an orientation switch. Given the development of two bilateral founder cells that generate a bilateral organism, a mutation that reverses the internal mirror orientation of those bilateral founder cells leads to inside-out development. The new orientation is epigenetically inherited by all progeny. A key insight is that each cell contained in the newly evolved organism with the internal skeleton develops according to the very same downstream developmental control network that directs the development of its exoskeletal ancestor. The networks and their genomes are are identical, but the interpretation is different because of the cell’s inverted orientation. The result is inside-out bilateral symmetric development generating an inside-out organism with an internal skeleton.
My first thought was…an interesting suggestion. We know from the homology of the patterning molecules involved that vertebrates and invertebrates are upside-down relative to each other, so at some point an ancestor flipped (or more likely, the ancestor was morphologically ambiguous in the dorsal-ventral axis), so let’s think about whether that’s feasible. And then my second thought was…wait, no way. That makes no sense at all.
So I read the paper. I was right, it makes no sense at all.
First thing I noticed was that the acknowledgements thank Francis Hitching, a notorious crank, Martin Brasier (no problem there, he’s a paleontologist specializing in Cambrian evolution…but also not a developmental biologist), and Cellnomica, a company that makes the modeling software. I looked. Eric Werner is the president and CEO of Cellnomica, which sort of means he was happily thanking himself for allowing him to use his software, which is nice, I suppose.
But except for Brasier, I’m already unimpressed. That doesn’t matter, though; he will sway me by the data and the evidence, right?
Next problem: there isn’t any. This is one of those totally evidence-free papers; the author didn’t bother to look up anything about the induction of skeletal elements in arthropods and vertebrates, cites nothing but three (!) papers all written by Eric Werner (!!), all published unreviewed in arXiv (!!!), and builds everything from a simplistic premise about how axis information is inherited epigenetically in dividing cells. There actually is a substantial literature on the inheritance of the orientation of cytoskeletal elements in dividing cells in flies and nematodes, for instance — but it’s not as trivial as what Werner proposes, and he doesn’t cite any of it, anyway.
The whole thing consists of the graphical output of simulation runs on his software, like this:
Orientation transform results in inside-out growth. The bilateral multicellular organism on the left Fig.a, where the red cells are on the outside, develops from the founder cells next to its right in Fig.b that have a Back-to-Back orientation. The reversal from a Back-to-Back orientation to a Face-to-Face orientation in the founder cells Fig.b is epigenetically inherited in the progeny. The result of this orientation switch is inside-out development seen in the organism on the right Fig.c where the red cells are on the inside. The transformation is reversible going in either direction depending only on the initial orientation of the bilateral founder cells.
He hasn’t even questioned his premises. Is there evidence of cells producing mirror-image progeny (actually, I recall that there is…but it’s not quite as uniform as he proposes)? Is there reason to think from, say evidence in the fossil record, that ancient chordates are inside-out arthropods? Nope, and Brasier should have been able to tell him so. Is there developmental evidence that this is how skeletons form? For instance, are the progenitors of internal skeletons homologous to the cells of the arthropod cuticle that produce there exoskeleton?
And that’s where I stopped and told myself, “obviously not”. The arthropod cuticle is produced by ectodermal cells that produce chitin. If you turned one literally inside out, the ectoderm would become the endoderm, the lining of the gut…a phylogenetically ancient tissue with homology between arthropods and chordates. It does not produce the chordate skeleton. That job is done by mesodermal derivatives…a tissue that forms in roughly similar ways by ingression/involution of cells during gastrulation in both groups. Mesoderm forms muscle and connective tissue in both arthropods and chordates, and produces bone and cartilage in addition in chordates.
The story is complete abiological and ahistorical bollocks. It’s really nothing but a pointless exercise in making a computer program run its paces, and is about as relevant to evolution as Spore, another game that attempted to model a science and failed abysmally.
It also makes me curious about something else: it was published in arXiv, which is mainly a repository of physics papers, with some abstract biological/mathematical stuff trickling in. Is the physics collection as plagued with drivel as the few samples of biology papers I’ve seen shoveled in there?
Werner E (2012) How to Grow an Organism Inside-Out: Evolution of an internal skeleton from an external skeleton in bilateral organisms. arXiv:1207.3624v1
(via Tommy Leung)
Inverting balloon animals?
So basically he started by assuming, based on nothing, that the various skeletons are homologous rather than analogous and extrapolated from there.
Fortunately, my chitin bones don’t break very easily.
On the other hand, I’m tired of lying in a heap on the floor*
Glen Davidson
*Oh don’t bother me over the fact that chitin’s stiffer than that.
There’s physics drivel in arXiv as well, but since physics/astrophysics is it’s primary game, the drivel/non-drivel ratio is much lower than for the biological science papers there.
I’d barely be considered a student of biology, and even I see that his thesis wouldn’t even make decent fertilizer.
As far as arXiv, that’s iffy. It’s run by Cornell University and while documents are not peer-reviewed, the authors are typically vetted by the university so they are known to at least be qualified to write on the topics. I do know that the Wikipedia considers arXiv to be in a grey area: it cannot be used to establish reliability of information but it can be used to supplement other, more reliable sources.
Turning my socks inside out does not make them into cardigans.
Does this sentence have some kind of meaning in the real world? Every time I come across the word ‘epigenetics’, it’s all blah blah blah… wtf? and too long to bother reading.
Seriously, help me out here. This scientific materialist wants to know: is there some kernal of truth at the bottom of this epigenetics thing?
And dogs are not cats that bark.
Weee! Biologgy is easy!
He just misspelt “magically”.
We really need a better methodology for storing, organizing, and ranking papers.
How about something that seems a bit more plausible, a single amino acid is the difference between a plowhorse and a million dollar harness racing champion … http://arstechnica.com/science/2012/08/single-mutation-keeps-racehorses-in-the-money/
re: arXiv – in most of physics and mathematics, it’s primarily as a preprint repository. In some fields, that’s its only function and anybody who uploads a paper that hasn’t been already accepted for publication would have a lot of explaining to do (that seems to be the case in my significant other’s area), and the bibliographical information is provided with the arXiv entry. I’ve heard rumors that in other fields it is sometimes used to establish precedence, i.e. as a place to deposit a working version of an idea you’re still in the process of fleshing out to protect yourself against plagiarism by being able to point to the datestamp to show that you said it first even if its not yet ready for publication. I’m also hearing that some mathematicians have been advocating and/or using it as a wholesale alternative to publishing behind paywalls, but the way things are, you probably need to already have a name before something thus “published” will be taken seriously by the rest of the community. They’re working on various concepts to implement some form of internal review process / vetting for papers (as opposed to the current and imperfectly implemented system of vetting for authors), though.
Overall, don’t throw the baby out with the bathwater! I think it’s a great concept with still a lot of room to grow, and even its shortcomings will prove very instructive on the move away from the current for-profit publishing model (which I hope will gain steam within the decade), and I’d very much appreciate if we had something like that in the cognitive sciences and more broadly life sciences.
Does this sentence have some kind of meaning in the real world? Every time I come across the word ‘epigenetics’, it’s all blah blah blah… wtf? and too long to bother reading.
Seriously, help me out here. This scientific materialist wants to know: is there some kernal of truth at the bottom of this epigenetics thing?
yes, epigenetics is a real phenomenon.
It sounds like rather than reading the extant lit on the subject, you might prefer NOVAs take on it, which was quite entertaining, if a bit out of date now:
http://www.pbs.org/wgbh/nova/body/epigenetics.html
…in short “epigenetics” simply refers to things that modify the expression of DNA, but not coded within DNA itself, and are still heritable.
there’s a long list of things like that that have been known about for decades (see, RE: methylation), it’s not magic or anything, though it HAS been misapplied in some circumstances to make idiotic unsupported hypotheses.
And dogs are not cats that bark.
ah, but the reverse might not be true!
;)
He has a model for the production of skeletons, which is his,
and is narrow at both ends…
If you revert the three layers of the initial embryo and let it fold the wrong way shouldn’t it get vital organs like heart and stomach on the outside?
“Fish are not inside-out insects.”
You’re right. That’s one of those sentences you just never imagine you’re going to need to say.
Exactly which animals’ skeletons are the figures in the simulation supposed to represent? To say that taking an animal with an external skeleton and turning it inside out would put its skeleton on the inside isn’t terribly insightful, and I don’t see how all this gee-whiz computer simulation has added to the idea.
Of course it makes sense that the Designer would repurpose exterior skeletons as interior ones. But lacking a Designer, evolution often doesn’t make “sense.” The development of novel features not something you can just figure out by just thinking about an organism and asking “how would I accomplish this?” One actually has to go out and look. The results are guaranteed to surprise you.
Novel features do not arise in order to solve environmental challenges.
Environmental challenges mean that variants incapable of surmounting them do not leave a genetic legacy. Random variation creates all kinds of novel features, most of which are crap. If one isn‘t and enables survival of the challenge, it persists.
In short, you have it backwards.
It’s like asking why Earth is so perfectly set up for us. Firstly, it’s by no means perfect. Secondly, and more importantly, if it were not supportive of life, people wouldn’t be able to ask such inverted questions. It’s as simple as that.
Echoing others:
The arXiv is primarily used by physicists and astronomers, so nonsense in those fields tends to get stamped out (although there was some nonsense from the crackpots at the so-called ‘Journal of Cosmology’ that made it through a while ago).
I usually put papers on the arXiv only after they’ve been accepted for publication elsewhere – it makes them immediately available to most of the likely audience, and does help in the rare cases that I’m worried about priority.
My personal rule for reading papers is to be very skeptical of anything that’s put on the arXiv without at least a line that says “submitted to _insert name of reputable journal_”.
Not if the designer is omnipotent or otherwise has unlimited resources. Human designers re-purpose existing things for economy’s sake – to save time designing or testing something new, re-use existing tooling, etc.
A designer with unlimited resources has no reason to re-purpose anything.
I aways suspected that I was T-dual to some kind of bug…
deep!
Here, let me try one:
Ectoprocts are not sideways hemichordates!
hey, this is kid of fun…uh…
Priapulids are not backwards holothuroideans!
no wait, they pretty much are…
I just want to say Spore also attempted to model fun with similarly disappointing results.
Even if this woul make sense: how the hell would this even evolve?
I’m not a scientist, but that sounds to me like one single mutation. Like, instant inside-out animal, instead of gradual change. Which would be pretty certain be not capable of living, too.
And even if one imagines an exoskeleton growing into the animal in order to provide additional load-bearing structures: what about moulting? And even if the skeleton got itsel separated in a part which stays inside and another one which goes, would such bones heal? If I remember correctly, arthropod skin contains glands which just create a substance, which then just hardens. Hm, it might work if the new bone glue gets inside the crack and hardens there.
Spore went pear-shaped, IMO, when they decided to make everything Disney cute. After that, it was all down the crapper. I don’t like the Disney cute thing, it makes me claustrophobic.
DaveL, but a perfect designer would be perfectly efficient. Or at least the thinking goes.
As a mathematician, I find arXive a very practical thing for:
* Uploading pre-prints to establish precedence: This is important for not-quite-finished work, and work that is submitted but still in the potentially year-long review/publication process. In some parts of mathematics, stealing ideas and trying to publish them before the original is quite common, and it’s sometime even done by reviewers deliberately stalling a paper while publishing the contents themselves.
* Uploading theses or small notes that are not something that a peer-reviewed journal would publish but could still be useful.
* Publishing a free-to-read version of an accepted paper.
So much for the fossil record.
Hey, Ichthic, thanks for the link.
I stand unconvinced about the heritability of epigenetic phenomena, though the implications for the expression of Natural Selection are profound.
Fish as inside-out insects. That’s on a par with vaginas being inside-out penes, right?
Tinjoe, don’t knock Spore. It’s provided us with hours of lolz.
I stand unconvinced about the heritability of epigenetic phenomena
then perhaps it’s time you moved on to the peer reviewed lit on the subject?
The statement about epigenetic transmission of components of axis specification is completely uncontroversial and trivial. All it refers to is the fact that a lineage of cells in development carries it’s history with it; it’s why when a dermal cell in your skin divides, it generates another dermal cell by default rather than a liver cell or a neuron or a bit of lung. Cells carry heritable epigenetic specifications that channel the differentiation of their progeny.
No, but the homology thing is the real deathblow. We now know that insects are part of a large group of protostome bilaterians that all share a molted cuticle. Arthropods (also onychophorans & tardigrades) add chitin to the cuticle, which makes it muscle-attachable and thereby an exoskeleton, but it’s fuly homologous with the protein cuticle of nematodes and ectodermal all the way.
The endoskeletons of fish have some ectodermal (dermal bone) components, but yeah it’s mostly mesoderm. Sucks to be all modelly-wrong.
Sucks to be all modelly-wrong.
lol.
i like that.
frustratingly though, you will not find this to dissuade a great many modellers about projecting their assumptions built into their models as if they were reality based.
David Sloan Wilson and compatriots come to mind as a recent glaring example.
I put the blame squarely on the fabric of the universe from which come the basic laws of physics (how the little bits of it work; more importantly, how the little bits of it work relative to each other according to local conditions, which, in a word is chemistry which, in turn, constrains the bits to relate in certain ways that are not always the same under all local conditions.
Sheesh, it’s not like atoms have free will but when it comes to them getting all orgy like in molecules! Once you’ve got some molecules, all bets are off unless you can constrain local conditions. Sadly, constraint is something that the universe has sorely neglected, what with all that clumping and isotropy and such irresponsibility.
Damn them molecules! They have no respect at all for the repercussions of their passions. They just weren’t raised right. Poor parenting on the part of the universe. Damn the universe for making us all inside out. I mean, why not just stop with arthropods already? They worked so well for so long and still make up the better part of macroscopic life. Life like us, don’t you realize? Successful and plenty hard and scritchy and crawling all over everything!
I really would feel so much better with my bones outside of me, wouldn’t everybody? Keeping the whims of errata and invention on the outside, cuddling me within, all safe and comfy and sleepy.
Damned universe . . .
Just more evidence that Eric Werner, like most deuterostomes, is talking out of his ass.
Are there any models pulled out of arses which explain the turtle’s unique skeleton?
@33 Ms. Daisy Cutter, Vile Human Being
I guess I should give credit to the creature creator, but that could be purchased separately. The full game was still a major disappointment and not fun.
Computer modeling – a powerful and sophisticated tool that is often used by people who have no idea what they’re doing. It’s like a brilliant electrical engineer has devised a new and superior kind of circular saw, but instead of showing the carpenter how to use it, or working together with the carpenter, he just walks into the woodshop and starts cutting everything to bits.
It reminds me of my time as a research assistant in grad school. I was assigned to the department chair’s pet project, writing a computer simulation environment for studying a certain human social behavior. When the whole thing was up and running and a bunch of students were using it to do small research projects I kept thinking it was a total nightmare. Everything result they got was totally dependent on their inputs and assumptions into the tool, they were learning nothing about the actual phenomenon. Only one student had the intelligence and creativity to formulate a question that the simulation environment could conceivably be used to address in a sound manner. My great fear was that the professor would latch on to one of the weak projects, get it published with me as a co-author and leave my name indelibly linked to crap research.
Thankfully that didn’t happen. I don’t know if he ever came up with anything to publish out of that project. He had one conference presentation, but cancelled it. If he did publish, he didn’t include me in the authors list.
*sigh*
PZ, didn’t you read the comments of the last thread about this?
First of all, it’s nothing short of sloppy to talk about “invertebrates” in this context. You mean arthropods. (If not specifically Sophophora melanogaster.)
In mollusks, the genes that do dorsal/ventral patterning in arthropods and vertebrates don’t do that; they’re not expressed only dorsally or ventrally.
Combined with a few other lines of evidence*, the most parsimonious conclusion by far is that nothing has flipped; arthropods and vertebrates have undergone some evolution in their patterning of the dorsoventral axis, and they happen to have done this in opposite ways.
* Like… vertebrates have 1 dorsal nerve cord, and arthropods have 2 ventral ones; but enteropneusts have 1 dorsal and 1 ventral one, mollusks have 2 ventral and 2 ventrolateral ones, and flatworms have 8 in total, arranged in an octogon: 2 ventral, 2 ventrolateral, 2 dorsolateral, 2 dorsal.
:-D
No, those* are mesodermal, too; the entire dermis is mesoderm, only the epidermis is ectoderm.
* The scales, and most of the skull and shoulder girdle and fin rays. And Silurian/Devonian oddities like fin spines and dermal pelvic girdles.
It might be even worse, but I don’t want to spend enough time on thinking through such nonsense in excruciating detail to find out.
:-D
Though, actually… that’s not really the case. In insects (arthropods?), the blastopore is ventral, then a stomodaeum and a proctodaeum form and the blastopore closes.
In vertebrates, the blastopore is caudodorsal, then the stomodaeum forms, the caudal neuropore closes over the blastopore, and then the proctodaeum forms. In short, your asshole isn’t your blastopore, and insect mouths aren’t blastopores either.
Incidentally, the caudal neuropore closes before the blastopore does. This leads to the transient existence of the canalis neurentericus, through which vertebrate embryos could shit into their own brains if they could already eat at that stage.
That page first claims the shoulder girdle of turtles is inside the ribcage, and then in the next sentence it says it’s part of the shell instead.
As far as the shoulder blade (the endochondral shoulder girdle) is concerned, both are wrong: it lies in front of the ribcage and inside the shell. The shell doesn’t consist of ribs and vertebrae alone.
The collarbones, though, form part of the shell.
Having the shoulder blades lie outside the ribcage instead of in front of it is more or less a mammalian specialty.
So… model… the ribs and the vertebrae are each fused to one dermal bone plate, and there are extra such plates around them. On the belly side, there are the collarbones, the interclavicle (an element of the shoulder girdle that marsupials + placentals have lost; it lies between the collarbones), and the gastralia which are direct descendants of “fish” scales.
I demand Comic Sans for that quote! No mercy!
So all you need is some paedomorphosis and you have an evolutionary explanation of creationists, MRAs and Republicans.
As much as I enjoy these takedowns (I learn a lot here), I enjoy even more the throw away lines that PZ inserts.
“He has a model for the production of skeletons, which is his,” an homage to M. Python and Miss Ann E. Elk.
Thank you for a great start to my day.
Well, there are pretty good data on the subject:
link
link
link
Thanks; that possibility was in the back of my mind as I posted but…(I hate when that happens).
Evolution from what? Was the urbilaterian then radially symmetrical, nervecord-wise?
Never mind. I remembered this post demonstrating developmental-program homology in deuterostomodorsal and protostomoventral nerve cords; then I saw that the only 2 surviving comments there are from you, ‘still not buying it’. (yes I just made up those adjectives)
Maybe it was like a flatworm; in which case, yes, radially symmetrical (octogonal).
Maybe it was like an acoelan or nemertodermatidan; in which case, similar but more chaotic.
Heh. Thanks for the link.
I don’t have time right now to find out if the work on cephalopods, by a certain Navet*, has been published; I attended a talk on it in 2009, I think. Work on flatworms and several other clades would be highly illuminating.
* Literally “turnip”.
web archive has moar comments, include from teh ECO:
http://web.archive.org/web/20100818173955/http://scienceblogs.com/pharyngula/2007/05/we_have_the_brains_of_worms.php
Thanks David! Of course I merely put the subtle inaccuracy in that joke to prompt an explanation of this relationship which had me confused for a while now.;)
So, one of those, ‘plausible, but we’d already studied that.’ thesis. Great.
Everyone had those, but this is why, when you have an idea like that, you ask someone who’s in that field already…
Never mind turtles. Can anybody explain Hero shrew spine?
No.
But Spore: Galactic Edition was put out be the National Geographic Channel, guaranteeing scientific accuracy and quality. I think they designed it to be released with their UFO programming, which is even better.
sigh
17 stoferb
That’s only if you turn them inside out starting from the chest cavity. If you turned them inside out from some bone marrow-
Well no, in this paper they’re trying to get from something like a bivalve to amphioxus- but only after I try and twist it into a form that makes more sense.
The latter doesn’t have a heart but rather just some blood that moves around as the animal moves so if you imagine all the organs similarly reduced and magically put a thin skin over it all you might think it was a reasonable inside out version of some sort of proto-clam.
But it’s clearly very easy to come up with problems for this just as soon as you flip on the critical thinking switch.
27 prae
Gradual change isn’t quite as much a requirement of evolution as what you’re implying. It only has to be gradual in that it takes place one step at a time (each step generally being beneficial but lacking that then at least not harmful enough to be selected out of the gene pool.)
In this case they’re proposing a single event that changes the cell state without changing the DNA sequence, which in itself is plausible enough, being something we can find a number of examples of in nature or lab settings.
I think though that they’re imagining this almost play dough sort of animal as the common ancestor for fish and insects, and as we know both exoskeletons and endoskeletons showed up in more complicated critters than that.
Aside from that the relevant line of thinking I’d also grant them is that bones would have changed quite a bit since the origin of the endoskeleton- maybe the poor quality of chitin as an internal bone wouldn’t be quite so damning before some nice mutations could amp the efficiency up.
-or at least I get the impression that’s the kind of thinking they are working with.
As always even if it’s plausible you need some actual evidence to then support it.
28 pipenta
I think the failure was more in the idea that decorating a lowly animal/tribe/city the way you decorate a room in the Sims would be very engaging.
51 Crissa
I’d say more “Plausible if we hadn’t already studied that.”