Pharyngula

Cephalopod development and evolution

i-4d425a46e484a6f847eb41d33bd3b294-ceph_tease.jpg

People are always arguing about whether primitive apes could have evolved into men, but that one seems obvious to me: of course they did! The resemblances are simply too close, so that questioning it always seems silly. One interesting and more difficult question is how oysters could be related to squid; one’s a flat, sessile blob with a hard shell, and the other is a jet-propelled active predator with eyes and tentacles. Any family resemblance is almost completely lost in their long and divergent evolutionary history (although I do notice some unity of flavor among the various molluscs, which makes me wonder if gustatory sampling hasn’t received its proper due as a biochemical assay in evaluating phylogeny.)

One way to puzzle out anatomical relationships and make phylogenetic inferences is to study the embryology of the animals. Early development is often fairly well conserved, and the various parts and organization are simpler; I would argue that what’s important in the evolution of complex organisms anyway is the process of multicellular assembly, and it’s the rules of construction that we have to determine to identify pathways of change. Now a recent paper by Shigeno et al. traces the development of Nautilus and works out how the body plan is established, and the evolutionary pattern becomes apparent.

Working out the development of a cephalopod is very hard work. They aren’t trivial to raise, requiring large quantities of filtered sea water and constant tending — imitating an open ocean environment in a tank in a lab isn’t easy. The Shigeno group has managed to raise 3 generations of Nautilus in the lab, which is an accomplishment in itself; they collected 1035 eggs over the course of five years, of which 81 reached the hatching stage. I think you can understand why most of us work with model systems rather than these difficult species. In my small zebrafish colony, I can get that many eggs in a week, and have well over a 90% hatching rate. Furthermore, it takes 8 months for a Nautilus egg to reach the hatching stage; that takes 2 days in a zebrafish. Ouch. The investigators have my sympathy. This is slow, difficult work.

The animals they were raising were Nautilus pompilius. If you need to be reminded of the differences between a nautiloid and a squid, here’s a handy reference diagram to their gross anatomy.

i-61e38947dec9cbb3fca182c2587982ef-ceph_anatomy.jpg
Comparative scheme of the body plans in nautiluses
and coleoids (e.g., squid), lateral view. The head complex is distinct from the visceral mass and mantle particularly in squid.
These schemes were described by the physiological orientation
defined by Hoyle (1886).

The affinities are clear. Both can be roughly divided into two body parts, a posterior visceral mass (that bag-like “head” of an octopus isn’t actually a head, it’s where it keeps its guts, and similarly the mass in these animals is within the shell or mantle) and an anterior head, with eyes and tentacles/arms and a collar and funnel. Nautiloids have a shell, simpler eyes, and more tentacles that lack suckers. These regions are set up early in development, and the purpose of this particular paper is to sort out what’s going on in just that head region.

Let’s get one confusion straightened out quickly. We usually think of the tentacle side as the front side, but embryologically, it’s the ventral side, and the visceral mass is dorsal. Just that swiveling around of perspective helps clarify the developmental process. In the picture below, you can see just how cute and adorable a baby nautilus is, but you can also see that the external morphology of the head complex is also the most complicated part of the animal.

i-e1ef5051b97d784a368c39c8cb59a1fd-ceph_baby_anat.jpg
Body plans viewed from the anterior, lateral, and posterior aspects, showing the large head complex with hood, eyes,
digital tentacles, and funnel. In contrast to Figure 1, these specimens are arranged by embryological orientation (see Fioroni,
1978), in which dorsal is towards the top of panel. Embryological dorsal 5 physiological posterior. Scale bars, 5 mm.

So now we roll back the clock and look at an earlier stage of development, at 3 months after fertilization. You have to imagine taking the animal above, putting one hand on top (dorsal), one hand on the bottom (ventral) and squishing it into a pancake-shaped disc. The picture in (a) below is looking down on the disc. The visceral mass, the mantle and shell field, is in the middle, and the more ventral head parts are now splayed out in concentric rings around the periphery.

i-37672b14a2cd461b05a716932e8c6a0e-ceph_3mo.jpg
A flat and less than 3-month-old embryo of Nautilus
pompilius
without outer yolk sac, DAPI staining. The embryo
has a total of five lateral compartments, composed of nine bud-like structures, on each side (I-III, yellow; IV and V, red). (a)
dorsal, (b) lateral, and (c) posterior view. The cephalic compartment (eyes, hood, and mouth) is shown by green. apr, anterior
projection. Scale bars, 300 µm.

Now you might be able to see some of the similarities to other molluscs. Another point of interest most easily seen in (b) is that there are little buds that will eventually form the tentacles — and there are nine on each side, for a total of 18. The primitive number of tentacles in cephalopods is thought to be 10, and what we can see here is that embryonically, each tentacle (except one pair in Nautilus) are formed from a pair of buds that are thought to fuse later in development.

One of the common hallmarks of papers describing the development of a species is the establishment of a staging series. Because the number of specimens is so small in this case, though, the staging is understandably a bit rough, and there aren’t a lot of detailed steps described. The process of tentacle bud fusion, for instance, wasn’t seen, and has to be inferred from widely spaced samples. The photos below show embryos at 3, 4, and 6 months, at least, and can give you a sense of the changes going on. And (h) in particular is very pretty — a kind of short, stumpy version of the later nautiloid to emerge.

i-27366a440f740529fcd090844c50a4c2-ceph_staging.jpg
(click for larger image)

Embryos 3 months (a-c), 4 months (d-f), 6-months-old (g-i) of Nautilus pompilius without the outer yolk sac and shell,
DAPI staining (a-f). The cephalic compartment (the hood, mouth, and eyes) is shown by green. The green arrowheads indicate differentiated cephalic compartments. The compartments for hood (I-II) and digital tentacles (III-V) are indicated by yellow and red,
respectively. The whole or partial mantle was removed in all embryos to expose the visceral mass, collar, and funnel. These
embryos are arranged by the embryological orientation. Dorsal (a,d,g), lateral (b,e,h), and posterior views (c,f,i). Scale bars, 200 µm
(for a-c; d-f), 300 µm (for g-i).

Tentacle/arm development and evolution is confusing! The authors compared Nautilus with a coleoid cephalopod, Idiosepius paradoxus. Idiosepius is a little strange itself; it’s a highly specialized, tiny (less than a centimeter long) squid with reduced arms that at least is prolific and easily harvested, and does represent the coleoids in this study. Nautiloids add additional tentacles beyond the basal 10 that muddle up the issue enough, but we can still see a core similarity. Idiosepius is shown in (e-g), and they also have 9 buds on each side, grouped in pairs (except for one). The irregularities in the distribution suggest to me that when we someday get around to identifying the molecular/genetic patterning elements in the cephalopod, we aren’t going to find a simple pattern generator—I suspect we’re instead going to find hard-coded specific regulatory elements for each arm.

i-b41a05fef0e01e3f55d7b652fb3f8123-ceph_naut_idio.jpg
Development of digital tentacles in Nautilus pompilius or arms in Idiosepius paradoxus embryos. (a,b) Early
arrangement of compartment III (yellow) and IV 1 V (red) in 3-
month-old Nautilus embryos (a, no. 020401; b, no. 020412). The
two buds in compartment V fuse to one as a bipartite arm,
whereas bud IV is still single. The arm base-like projection of
thick tissue is present (an arrowhead in a). Asterisks indicate
newly differentiated tentacle buds. (c,d) Digital tentacles in the
3-month- (no. 020326) and 4-month-old (no. 020304b) embryos
viewed from the ventral aspect without outer yolk sac. Derivatives of the cephalic compartment, lateral compartments I-III,
and IV 1 V are indicated by green, yellow, and red, respectively.
The buccal tentacles (buc) appear in a 4-month-old embryo
(blue in d). A large projection is present toward the anterior
(see apr) to form a base of the medial side of the digital tentacles. Asterisks indicate small buds considered to be newly
formed tentacles. The digital tentacles arranged with similar
topological manner are indicated by dotted lines. apr, anterior
projection. The identity of compartment III is unclear. Hoechst
nuclear staining (a-d). (e-g) The scanning electron micrographs
show the early arrangement of arms and arm bases in I. paradoxus (e, stage 20, lateral view) compared with 3-month-old
embryos of N. pompilius (Fig. 3b). In Idiosepius (f, stage 21; g,
stage 24, posterior views), the two buds of a bipartite arm (I-III, yellow and V, red) fuse into one arm anlage except for IV
(red) in later stages. The arm bases begin to cover the eye
region to form a head-foot complex (arrowheads, red). The
developed cephalic bulges (ceb) are shown by closed dot lines
(in e, the head compartment is shown by green). fu, funnel.
Scale bars, 200 µm.

One other question people always ask — we’ve got mostly ten-armed squids, and eight-armed octopus. What happened? We don’t know. The paper briefly discusses the homologies between different species, but unfortunately the homologies in the octopods seem to be an open question, still, with different competing explanations. Obviously, what we need is more octopus embryology!

i-414f738ae529d09e005806903f87ac5f-ceph_arm_pattern.jpg
Comparative scheme and arm homologies in Nautilus and coleoid cephalopods. The plesiomorphic arrangement of
arms in coleoid cephalopods is considered to be 10 equal arms
on each side with the five bipartite arm condition (Roman
numerals) shown as a cephalopod phylotype composed of shared
characters. In Nautilus, tentacle anlagen IV and V have a
unique differentiation manner. Other species have a conserved
five arm formula (I-V) except lack or degeneration of arms
[Vampyroteuthis;
Octopoteuthis, asterisks indicate the
adult stage] and delay of differentiation timing in each arm
during the early ontogeny (arm IV in the embryos of Idiosepius
paradoxus
), arm III and V in the embryo and paralarvae of
Todarodes pacificus. In octopodiformes, there are some unsolved hypotheses
for arm homologies. In Octopus, the Arabic numerals indicate arm for-
mula adopted by each author.

At least when comparing nautiloids and coleoids, we aren’t completely lost. The similarities in the organization at that early pancake-like stage are easy to see, and are color coded in this diagram.

Note also how the arm buds are initially located posteriorly and the mouth anteriorly, like a more typical descendent of a bilaterian worm. Later in development, the arms migrate to wrap around the mouth, to produce the familiar central mouth surrounded by arms.

i-c8dc5ce675e6babdde0a1d472e9066f8-ceph_naut_squid_comp.jpg
(click for larger image)

Comparative scheme in the early embryonic bodies between the
Nautilus and squid. Similar characters are represented by the same colors (e.g., the cephalic compartment and brain cords are
shown by orange and red, respectively). Bipartite arms are indicated by dotted lines.

Now to answer that question raised at the beginning of this article: what is the evolutionary relationship between the organization of a primitive gastropod and a cephalopod? The diagram below relates the parts of Patella, more familiarly known as a limpet, to Nautilus and Idiosepius, and also within the cephalopod group. What cephalopods did was modify the muscular gastropod foot into an array of tentacles, and then elaborate the set of organs above them (eyes, ganglia, funnel, etc.) into a head complex.

i-69b51dcc37e8cddd50aa8fbd8ebc1af2-ceph_evo.jpg
(click for larger image)

A suggested alternative scenario for the evolution of the cephalopod head complex by assembly of multiple molluscan
body parts. (a) Simplified schematic figures of conchiferan body-plans to show comparable and derived features. (Each color represents suggested homologous parts in a primitive form of the gastropod Patella, Nautilus, and a representative derived form of the coleoid Idiosepius. The homologies between gastropod “head” part
and cephalopod cephalic compartments are not certain (the orange color). The similar topographical arrangement of body plans is
emphasized for comparision. (b) Cephalopod body plans are characterized by elaboration of the head complex. The arm bases cover
the whole head part and funnel fused to them to originate a more integrated head-arm part in coleoids
(only the transient condition is represented in this figure). No such cover is identified in Nautilus embryo, although some arm-base-like structures develop during tentacle formation. Homology inferences are still controversial, but loss of arm II in octopodiformes (or vampyropods) composed of vampyroteuthids and octopods, might occur as seen in late embryos of a basal coleoid, vam-
pire squid. ab, arm base; olf, olfactory organ; rhi, rhi-
nophore.

We can also sketch out the molluscan body plan and see the relationships in the phylotype of gastropods and cephalopods. The ironically amusing part is that what we’re calling the “head complex” of a squid is actually derived in part from the foot — it’s an amazing piece of of morphological juggling that actually makes a heck of a lot of sense from a developmental point of view.

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(click for larger image)

A conchiferan and cephalopod phylotype is composed of shared morphological characters to show a drastic transition
from the benthic to nektonic forms. These figures indicate that the cephalopod tentacles and arms are derived from the ancestral
foot. Morphological novelty is seen in the appearance and elaboration of collar-funnel compartments as a part of the head complex
(black). The various organs including cephalic compartment (orange) and neural cords (red) are assembled to form an integrated
head complex along the anterior-posterior body axis.

This was an awesomely data-rich paper, and I haven’t even touched on some of the information on gene expression, so I’m just going to give you the very handy brief summary from the end of the paper.

  1. The tentacles/arms were derived from the foot
    region. Acquisition of a nektonic life from a
    benthic ancestor accelerated the loss of a creeping pedal sole and the development of tentacles
    from a freely mobile foot.

  2. In an ancestral cephalopod, the number of ten-
    tacles/arms was five pairs (or 10 pairs of bipartite
    arms). This means that the large number of tentacles in Nautilus results from secondary multiplication. Alternatively, the 10-arm condition of
    coleoids could be neotenous.

  3. The mouth surrounded by foot-derived tentacles/arms is unique among molluscs. This
    body plan was created by enwrapping the head
    part by epidermal tissues of pedal origin. During embryogenesis the pedal region shifts for-
    wards on the body surface, and eventually the
    “foot” is displaced anterior to the head.

  4. The rhinophores of Nautilus and olfactory
    organs of coleoids are presumably homologous,
    since they develop at similar posterior parts
    of the cephalic compartment as discussed earlier. Therefore, ancestral olfactory organs might
    have been present at an early stage of cephalopod evolution.

  5. An unfused hyponome as a primitive funnel
    might have arisen from the posterior part of the
    hood-collar compartment, which is possibly
    derived from an intermediate zone between the
    head-foot and visceral mass in the monoplacophoran ancestor. Alternatively, there
    is a possibility as suggested by Naef that
    a region of epipodial (dorsal) tentacles may differentiate into the hood-collar compartments.
    Then, with modifications for free-swimming
    behavior, the collar became distinct at the lateral region of the mantle and well-developed,
    including the funnel.

  6. Cephalopod brain masses centralized from the
    primitive tripartite neural-cord condition
    as seen in the embryonic nervous system of
    coleoids. Early cephalopods probably had a
    cord-like brain (not ganglia) as is found in the
    pedal cords of primitive gastropods.

  7. The optic lobes innervating cerebral eyes were
    derived from the cerebral cord, since this connection is found in the early embryos of Nautilus.

  8. The hood seems to be a secondarily-derived
    structure, convergent with the operculum of
    gastropods, which was coopted from two dorsal
    arm pairs together with ocular tissue and part
    of the collar/funnel complex.

  9. The ancestral function of transcription factor
    engrailed was conserved during the shell formation process, given that similar expression patterns were seen in Nautilus, Idiosepius, and
    other molluscan embryos. Further
    analysis is required; however the expression
    patterns may suggest a role for arms (pedal
    components), funnel, collar, and eyes in the evolution and development of molluscs.

The whole system is beautifully complicated, but what we see in this work is the power of developmental biology to illuminate the underlying, fundamental rules that define the evolution of organismal form.


1:
Shigeno S, Sasaki T, Moritaki T, Kasugai T, Vecchione M, Agata K. (2007) Evolution of the cephalopod head complex by assembly of multiple molluscan body parts: Evidence from Nautilus embryonic development. J Morphol. [Epub ahead of print].

Comments

  1. #1 silence
    July 30, 2007

    I’ve now got visions of a cannibal asking a creationist to taste various primate species, and saying “see: we taste as much like a chimp as a Mallard tastes like Muscovy”

  2. #2 Brownian
    July 30, 2007

    “a flat, sessile blob with a hard shell”

    I didn’t have time to read this entire post. Is it about conservatives?

  3. #3 Tom @Thoughtsic.com
    July 30, 2007

    Wow, that is beautiful. Just goes to show how a little change can truly go a long way, especially evolutionarily.

    I like these posts because while most of us come here as a sort of discussion of atheism and combating ignorance, a post like this comes out and teaches us something. If not for this post, I honestly wouldn’t have had a clue that oysters and squid were so closely related. Not only interesting but educational.

    I appreciate it.

  4. #4 Jsn
    July 30, 2007

    I was, and still am a Gould fan. He is why I love science blogs.
    This is wonderful stuff but it’s too bad that the major responses only come from book desecration and atheist ethics/deportment posts.
    Thanks, PZ. Some of us are here for the science too, even if we aren’t scientists ourselves.

  5. #5 PalMD
    July 30, 2007

    The real question is what is the best stage at which to eat one with butter, and would Gould sit down with Creationists over coffee and cephalopods.

  6. #6 Paguroidea
    July 30, 2007

    Ooooooh! Awesome. Thanks for the post, PZ. I appreciate all the time you put into explaining the research.

  7. #7 Jeff
    July 30, 2007

    PZ, how much has DNA testing shuffled around the traditional cladistic taxonomies (hopefully my terminology is correct)? If at all? I had heard some rumblings of this when DNA testing was first being developed, but not much since.

  8. #8 Schwa
    July 30, 2007

    Is there a useful primer for basic cephalopod embryology? I get the feeling that the pictures would be a lot more comprehensible if I knew the first thing about development in something that wasn’t xenopus or drosophila.

  9. #9 Darby
    July 30, 2007

    I’ve found snail eggs with pre-shelled embryos to be a good lab demonstration of mollusk relatedness – there’s a similarity to the last figure, but the gastropod food is more blobby at that stage than flat, suggestive of tentacle buds, and the visceral mass without a shell (and precoil) looks a lot like an octopus “head.” We don’t go into details – it’s a basic zoology course – beyond making the point that similarities in embryos can point to relatedness when adults don’t much resemble each other. When a group has a good grasp of evolutionary principles, you can also talk about the eggs as being a particular environment that isn’t that different among the different molluscs, so the basic forms haven’t shown as much breadth in adaptation as the adults.

  10. #10 derek
    July 30, 2007

    (although I do notice some unity of flavor among the various molluscs, which makes me wonder if gustatory sampling hasn’t received its proper due as a biochemical assay in evaluating phylogeny.)

    Is that why tetrapods taste like chicken?

  11. #11 Graculus
    July 30, 2007

    Is that why tetrapods taste like chicken?

    No, chicken tastes like tetrapod.

    Annals of Improbable Research, Vol 4 No. 4. (July/August 1998), has a great article on the evolutionary relationships of flavours.

  12. #12 Patrick C
    July 30, 2007

    This answers a question I have been wondering about for a while: why is the stomach of the squid at the pointy end and the anus back near siphon and gills.

    Nifty. Thanks PZ.

  13. #13 Steviepinhead
    July 30, 2007

    At the risk of becoming the target for a certain Turkish creationist book distributor, the pictures were exceptionally pretty! Now disqualifying myself as a recipient of Turkish coffee-table tomes, however, your pictures were also data-laden and powerfully explanatory.

    I have to agree with the other commentators–while the invigorating intellectual debate here is the very thick and tasty meringue, it’s that underying layer of dense and yummy science that keeps me coming back here for more.

    Thanks, PZ!

  14. #14 Adam Peter Stein
    July 30, 2007

    Does anyone know how nautiluses taste? Do you present them with clarified butter or do you batter-dip them? Grappa, pinot noir, or sparkling wine?

  15. #15 Disgusted in St. Louis
    July 30, 2007

    Thank you for this post PZ. This post and the comments brought back memories of a biology adventure I undertook about 40 years ago, as my semester project, following the development of fresh water snails. I wonder whatever bacame of my lab book with all the hand sketches of observations under the microscope — it would be amusing to look through if I could find it. Probably remained with the instructor just like the set of pressed plants of native Missouri flora from my botany project.

    DNA testing must be an immense help in evaluating phylogeny because of the confusion resulting from gustatory sampling due to “tastes like chicken” syndrome. ;^)

  16. #16 Despard
    July 30, 2007

    Beautiful! Many thanks for this, PZ. Coincidentally I have just watched the ‘Ocean Deep’ segment of the wonderful Planet Earth where the habits of the Nautilus get a bit of screen time.

    It also contains such enchanting creatures as the aptly-named Dumbo octobus, and the strange and eerie bioluminescent vampire squid from hell (Vampyroteuthis infernalis). Well worth a look for cephalopod afficionados, although it does linger for a while on a few of those irritating cetaceans…

    Seriously though. Awesome show.

  17. #17 LKL
    July 30, 2007

    Like Schwa, I’d love to see a primer of molluscan development- I’d like a comparison of everything, though, from bivalves to abalone to squid. I spent a few hours searching the net once, but never found anything definitive. This is by far the best I’ve seen.

  18. #18 Sepiida
    July 30, 2007

    The question being: are Turkish coffee-tables, in addition to bearing tomes, also know to carry platters of calamari?

  19. #19 Torbjörn Larsson, OM
    July 30, 2007

    Awesome, even though the reasons for the gastronomic advantages of molluscs, if any, is still unexplained.

    Is that why tetrapods taste like chicken?

    Tetrapods outside most mammals, you mean?

    PZ sez: “Hold your molluscs at arm’s length, but your tetrapods closer – they aren’t as wet.” But he still uses the same platter, I bet.

    Say, why did tetrapods cross the beach?

  20. #20 Torbjörn Larsson, OM
    July 30, 2007

    Awesome, even though the reasons for the gastronomic advantages of molluscs, if any, is still unexplained.

    Is that why tetrapods taste like chicken?

    Tetrapods outside most mammals, you mean?

    PZ sez: “Hold your molluscs at arm’s length, but your tetrapods closer – they aren’t as wet.” But he still uses the same platter, I bet.

    Say, why did tetrapods cross the beach?

  21. #21 arachnophilia
    July 30, 2007

    No, chicken tastes like tetrapod.

    no, chicken tastes like crocodile, which likely has a similar flavor to basal tetrapods.

    also, iirc, there’s a lot of good arguments here paleontologically, specifically involving ammonites and orthoceratids and such.

  22. #22 VWXYNot?
    July 30, 2007

    I do notice some unity of flavor among the various molluscs, which makes me wonder if gustatory sampling hasn’t received its proper due as a biochemical assay in evaluating phylogeny

    This would be the perfect career for an ex-colleague of mine who has set out to eat members from as many different branches of the evolutionary tree as possible. His traditional hand-made leaving card from the lab was a huge phylogenetic tree with checkboxes next to each branch to indicate a successful tasting experience.

  23. #23 frog
    July 30, 2007

    PZ: “The irregularities in the distribution suggest to me that when we someday get around to identifying the molecular/genetic patterning elements in the cephalopod, we aren’t going to find a simple pattern generator–I suspect we’re instead going to find hard-coded specific regulatory elements for each arm.”

    Maybe but… Have you read Wolfram’s book “A New Kind of Science”? It has some pretty nice explanations of why a simple mechanism can lead to very complicated, irregular results that are practically impossible to reverse-engineer from the end-products. It only takes a few components with non-linear couplings to produce data that appears extremely complex and would never have been predicted from the components (or visa versa).

  24. #24 Alan Kellogg
    July 30, 2007

    #5

    At this stage of existence Gould is far more likely to be interested in brains.

  25. #25 Patrick Quigley
    July 31, 2007

    One other question people always ask — we’ve got mostly ten-armed squids, and eight-armed octopus. What happened? We don’t know.

    Ah ha! So science can’t answer every question. It is therefore completely useless.

    The paper briefly discusses the homologies between different species, but unfortunately the homologies in the octopods seem to be an open question, still, with different competing explanations.

    Double ah ha! Clear evidence that evolution is the subject of controversy even among scientists, and so must be completely wrong.

    And if evolution is false then my Holy Book (but only the version that I use) must be literally true (but only if you use my interpretations).

    Thank you Magic Man, for providing such an unambiguous and easy alternative to the complexities of biology!

  26. #26 arachnophilia
    July 31, 2007

    is this predatory thing common among biologists? my paleo prof would occasionally regale the class with stories about a “great phylogenetic eat-off,” some kind of competition that was one part specimen-collecting, one part face-stuffing, one part fear-factor. apparently, the person with the most phyla consumed would win.

  27. #27 Peter Ashby
    July 31, 2007

    Sepiida

    From my experience (two weeks in Kusadasi on the West Coast near Ephesus) the Turks are not culturally into seafood. They do however really know how to cook terrestrial tetrapod meat, mmm mmm!

    However we took a day trip from there to the Greek Island of Samos literally just off the coast, you can see it clearly from Kusadasi and we sat in a waterfront Taverna and I ate what the French would call a Plat de fruit de mare, including both calamari and wonderfully crispy baby octopus. I shared it with the eldest spawn and it along with a carafe of retsina was much appreciated. I saw nothing like it in Kusadasi. Which shares the same waters.

  28. #28 hoary puccoon
    July 31, 2007

    Peter Ashby–
    It’s ‘fruit de mer.’ A ‘mare’ is a pond ‘aux canards’ (which taste like a cross between chicken and tetrapod.)

  29. #29 James Collins
    July 31, 2007

    The author wrote:People are always arguing about whether primitive apes could have evolved into men, but that one seems obvious to me: of course they did! The resemblances are simply too close, so that questioning it always seems silly.

    My comment:
    This type of logic is common throughout the flaky theory of evolution. Using the logic of this author we could ‘safely’ assume that a platypus is closely related to a duck, which is an absurdity of course.

    All living entities are extremely sophisticated and extremely complex, from the so-called simplest cell to the intelligent human.

    And you can’t rely on examining the DNA; The number of genes and the length of the DNA has very little to do with identifying a life form, they skip all over the scale, it certainly is not a tool of science.

    In fact there is NOTHING in the field of evolution that can be called science but the mechanical equipment that some scientists use, like a microscope for example.

  30. #30 harold
    July 31, 2007

    Ignoring the creationist troll post immediately above, I would like to suggest that…

    “one can believe in god and accept evolution and reality and even be a scientist.”

    Do others here agree?

  31. #31 Peter Ashby
    July 31, 2007

    Harold, James Collins makes several claims that are not only wrong they display his ignorance. No competent anatomist would classify a platypus as being closely related to a duck (though they are more closely related to ducks than we are). He is clutching at a caricature to try and make his point.

    His other point about dna is obviously wrong to anyone who has any knowledge of genetics. My own work has been very much to do with for eg Hox genes and these genes and the clusters they come in are exemplars of metazoan evolution. They have even been shown to be functional in other animals. James Collins is as I have said simply displaying his ignorance. If evolution is not true then nothing in modern biotechnology would work. I would not be able to use the sequence of a gene in one species to pull out that gene from a distantly related species. I have personally for eg cloned chicken versions of mouse genes using the mouse sequences as probes. I did it in a lab where a co-worker was pulling out dogfish genes using a whole slew of sequences from different sources.

    They published it in Nature:
    http://www.nature.com/nature/journal/v416/n6880/abs/416527a.html

    The fact of evolution enabled a question about evolution: how did fins become limbs? to be asked.

  32. #32 Justin Moretti
    July 31, 2007

    #29: Yes, absolutely.

    What one believes about the metaphysical does not have to affect one’s thinking on reality.

    How one views the meaning of life and subsequently faces death need have no bearing on how one explores and understands the physical world in between.

    To me, the fact that “God has given us brains” (to use the phrase very loosely) indicates that we are supposed to use them to understand the Universe. Trying to enforce or promote ignorance would therefore constitute grave transgressions upon the Will of God. Next time there is a Dover-type trial, there is nothing I’d like to see more than a devoutly Christian judge tearing the Creos to pieces on this very point. I think that would devastate them more (at least in psychological terms) than any legal judgement.

  33. #33 hoary puccoon
    August 1, 2007

    James Collins’s comment, ‘the number of genes and the length of DNA has very little to do with identifying a life form, they skip all over the scale,’ is a perfect example of why I despise creationists.
    Collins is factually accurate on that– the SIZE of genomes does skip around. That means, of course, that somebody in the creationist camp read and understood the literature. So they must have also learned that the CONTENT of DNA shows regular similarities between species that correspond precisely with lineages worked out on the basis of comparative anatomy and fossil evidence.
    In other words, creationists must have known they were lying when they came up with that point.
    That is where my stomach starts churning. What kind of slimy bunko artist comes up with a scam whose ultimate victims are public school children? Selling marijuana in school parking lots is more honorable than being a creationist.

  34. #34 jotetamu
    August 1, 2007

    I never thought the day would come when James Collins would have a new idea and post something other than a version of his “if you want to prove evolution, build a living cell from chemical elements” post. But I suppose he had to start something new, after that evolved into the version “build a cell and you will have both proved and disproved evolution”, posted to Neurologica a few days ago (http://www.theness.com/neurologicablog/default.asp?Display=141).

    Jim Roberts

  35. #35 jotetamu
    August 1, 2007

    I’ve just noticed that James Collins (Anonymous) posted the shorter version yesterday at Sandwalk (http://sandwalk.blogspot.com/2007/07/another-bad-review-of-edge-of-evolution.html),
    that is, without the addition that building a cell from scratch would disprove evolution.

    Jim Roberts

  36. #36 Arnosium Upinarum
    August 1, 2007

    Just plain WONDERFUL. My hat off as I bow, PZ. Absolutely beautiful stuff. Not only do we get a neat yet rich peek into the intricacies of devolopment (multicellular assembly as well as the implications for long-term evolution) but we also get a little serendipitous bonus on the side to remind us of our anthropomorphic conceits and prejudices:

    “We usually think of the tentacle side as the front side, but embryologically, it’s the ventral side, and the visceral mass is dorsal. Just that swiveling around of perspective helps clarify the developmental process.”

    It also makes me think of how incredibly silly our notions about what forms complex extraterrestrial life may take…we often use the phrase “life as we know it” as if we completely understood everything there is to know about life on EARTH! We obsess over “aliens”, yet we are already surrounded by them: they are alive and flourishing right here on our very own little planet. In fact, we don’t even “know” OURSELVES. WE ARE the nearest aliens.

    I like anything that shaves our arrogance and conceit down several notches. There’s nothing bad about being shown how mistaken we are. It just makes us smarter, and stronger for it, that’s all. Religionists have forsaken this very valuable and HUMAN way of learning their way through nature. They consciously PREFER to remain ignorant. Religion is nothing more than a medieval castle-fortess with a mote designed to keep nature out of the mind.

    These items are positively addicting. More please.

  37. #37 Arnosium Upinarum
    August 1, 2007

    AARRGGHH.

    Pardon. A paragraph just after the PZ quote was inadvertantly deleted. Here it is:

    That kind of “swiveling around of perspective” is an important attribute of what human brains have evolved to do, and they are good at it. The IMAGINATION is involved. That’s what its for. Too bad so much of that innate talent is either hijacked for superstitious nonsense or squelched outright by cultural pressures of one kind or another.

  38. #38 harold
    August 1, 2007

    Thanks for the replies.

    I was going to point out to James Collins that –

    1) We can tell that ducks and platypi are not related by applying the same scientific techniques that tell us that humans and apes are related and …

    2) His comment about DNA was one of the most bizarre things I have ever seen. Only someone who knows nothing about DNA would make a comment like that. When I see something like that, I have to wonder if it’s original or an attempt at repeating something from a creationist site that the poster just didn’t understand (why don’t they just link the sites instead of plagiarizing them?).

  39. #39 harold
    August 1, 2007

    The reason for my odd question, above, about religion was that I shamefully let myself get involved in one of the inevitable atheists vs non-atheist wars at PT (in fact I more or less started it). My question wasn’t related to James Collins’ badly misguided post.

    For full disclosure –

    I don’t care what other peoples’ private religious beliefs are as long as they don’t try use said beliefs as a justification to violate my rights and/or promote irrational social policy.

    Therefore, although I’m not a creationist, and don’t consider myself an atheist either, I have a problem with creationists, but not with atheists.

    Although it is irrelevant what I think, I consider atheism, especially the secular humanist variety, to be an entirely rational perspective, and fully compatible with the highest ethics.

    In fact, the majority of my best friends are self-described atheists, and that’s been true probably since junior high school.

    However, although I don’t believe in heaven, hell, miracles, angels, anthropomorphic gods, or the like, personally, I’m more of Unitarian Universalist.

    I also feel that, although I don’t personally follow a formal traditional religion, people who do so are not necessarily deluded, delusional, irrational, or intellectually dishonest. From the biology universe, I would offer Francis Collins and Ken Miller as examples that support my position.

    The reason I began following the public issue of evolution in (public) school curricula was because of the Kansas 1999 incident, when a creationist school board sought to remove evolution from the curriculum.

    Although atheists have a complete right to express themselves, in whatever language and style they choose to, I have occasionally given in to annoyance when there seems to have been a mushrooming of what I, entirely subjectively, perceive as an endorsement of exaggerated and intolerant language on the part of pro-science individuals who self-identify as atheists.

    Of course, it doesn’t really matter, since no atheist is trying to take my tax dollars and use it to teach kids politically-motivated sectarian garbage as “science”.

    So why did I post that question here? Another pro-science poster, whose posts I respect and whose religion or lack of religion I have no clue about, suggested that it would receive a hostile response, and I concurred. Others denied this, and insults flew. Finally, I pointed out that we could test this assertion, instead of merely conjecturing (and hurling insults around). Why “think” when you can do the experiment?

    I did a very uncontrolled and not very well-designed “experiment”, posting the question here and seeing what happened. I haven’t left it up very long. Still, the bottom line seems to be that at least this time, with the caveat that this experiment wasn’t done very well, a hostile response was not generated.

    Which is fine with me. I’m willing to terminate the experiment now (although of course the post may continue to generate replies). The prediction I endorsed was not the observed outcome, but in this case, I’m quite happy with that.

  40. #40 Torbjörn Larsson, OM
    August 2, 2007

    harold:

    “one can believe in god and accept evolution and reality and even be a scientist.”

    Absolutely. It is then one changes the science to pseudoscience, for example by inserting teleology, that it becomes problematic. I would also argue that a biologist that has two versions of evolution, one in the laboratory and one privately but publicized, is incompetent at what he does.

    From the biology universe, I would offer Francis Collins and Ken Miller as examples that support my position.

    Both of these are doing something else than you claimed earlier though. They are inserting teleology into a theory that doesn’t predict it from the current data.

    Don’t you think you are confusing your clearly stated position from earlier from what people actually do, and that you at times formulate the later? That would surely start a discussion on the irrationality and anti-scientific taint of the later position.

    Jim Roberts:

    I’ve just noticed that James Collins (Anonymous) posted the shorter version yesterday at Sandwalk

    And, IIRC, he also drove by Panda’s Thumb and posted the longer inconsistent one.

  41. #41 Torbjörn Larsson, OM
    August 2, 2007

    harold:

    “one can believe in god and accept evolution and reality and even be a scientist.”

    Absolutely. It is then one changes the science to pseudoscience, for example by inserting teleology, that it becomes problematic. I would also argue that a biologist that has two versions of evolution, one in the laboratory and one privately but publicized, is incompetent at what he does.

    From the biology universe, I would offer Francis Collins and Ken Miller as examples that support my position.

    Both of these are doing something else than you claimed earlier though. They are inserting teleology into a theory that doesn’t predict it from the current data.

    Don’t you think you are confusing your clearly stated position from earlier from what people actually do, and that you at times formulate the later? That would surely start a discussion on the irrationality and anti-scientific taint of the later position.

    Jim Roberts:

    I’ve just noticed that James Collins (Anonymous) posted the shorter version yesterday at Sandwalk

    And, IIRC, he also drove by Panda’s Thumb and posted the longer inconsistent one.

  42. #42 Z.C. Z.,C.
    August 2, 2007

    It’s hard for me to understand why we have battlefield for “atheists vs non-atheists” war on a blog about biology. As far as I can see both sides look equally irrational. On one side I see clowns ready to perpetualy lie only to justify their political agenda (and not at all interested in biology or development). On the other side I see “if we prove there is no God, all our problems with creationists will be solved”. Both sides have 0 chance to make their point in my view.
    Even if somebody proves nonexistence of God, creationists may just turn into some other -ism and continue harrasing someone else. They have problem with (american) society, not with Darwin. Religion provides just an easy and cheap weapon to mobilize masses.
    I beg all scientists here, stop wasting bandwidth by attacking God (because something metaphysical can not be measured by science or scientists) and religion (all of them are just as bad or good as humans contributing them, so veeery far from perfect). Attack lies and dishonest people, you’ll find them even among scientists.

    If a beaver builds a dam it is called “extended phenotype”. If a human builds a church/mosque/temple atheist scientists just call it stupid because there is no God. It’s obvious creationists are big threat for educational system but I think that (atheist) scientist should also ask questions like “if the humanity is devouting so much time and energy to religion what kind of evolutionary advantage it brings?” or “which gene is resposible for this disorder?” or “if huge majority has this disorder can we call it disorder at all?”.

    Answer for Harold: Sure!

    Catholic from a small european country

  43. #43 hoary puccoon
    August 2, 2007

    Harold, Peter Ashby,
    Take a look at James Collins’s ‘bizarre’ statement about DNA again. It’s not ignorant– it’s snaky. It is trivially true that ‘the number of genes… has very little to do with identifying a life form.’ In other words, you can’t tell which organism you have by simply knowing it has, say, 25,000 genes.
    That much is true. But how could someone have learned that relatively minor point without also learning about the huge amount of work of the kind Peter describes, in which DNA analysis is vital? I don’t believe it could happen. For that reason, calling people like Collins ignorant is far, far too kind. Try to think more in terms of ‘evil’, guys.

  44. #44 harold
    August 2, 2007

    From the biology universe, I would offer Francis Collins and Ken Miller as examples that support my position.

    Both of these are doing something else than you claimed earlier though. They are inserting teleology into a theory that doesn’t predict it from the current data.

    I did not realize that either Ken Miller (who has done a lot of good defending mainstream science from ID and creationism) or Francis Collins was making teleological arguments.

    I am quite opposed to inserting teleology into science. I’ll have to do some reading on the exact positions of Miller and Francis Collins in this regard, and be more careful about using them as examples. However, they do seem to be able to contribute quite a bit, so presumably, we’re dealing at a subtle level here.

    Of course, I’m refering to Francis Collins of the Human Genome Project, not James Collins, who contributed an irrational creationist post above.

  45. #45 harold
    August 2, 2007

    In fact, Collins does seem to subscribe to some teleologic views that I disagree with quite strongly, although my disapproval of these isolated ideas is outweighed by my admiration of his contributions to science.

    The blockquoted stuff below is merely cut and pasted from the Wikipedia article on Collins.

    His own belief system is Theistic Evolution (TE) which he prefers to term BioLogos. BioLogos rests on the following premises: (1) The universe came into being out of nothingness, approximately 14 billion years ago,

    Putting aside the issue of “nothingness” and the very approximate nature of the dating, this seems fine.

    (2) Despite massive improbabilities, the properties of the universe appear to have been precisely tuned for life,

    This is a logical fallacy, although Dr Collins is not the only highly productive and intelligent scientifically trained person I know of who makes this odd mistake.

    Since we’re already here, and looking back, we cannot possibly see anything other than a history of a universe which is suited to the emergence of human life. That doesn’t tell us anything about how probable or improbable it was a priori.

    Nor, even if we somehow knew that, at some sort of non-deterministic branching point in the past, it was “improbable” for the universe to have turned out the way it did, would that in any way imply supernatural intervention. By definition, something that has any probability greater than zero is something that could happen naturally.

    (3) While the precise mechanism of the origin of life on earth remains unknown, once life arose, the process of evolution and natural selection permitted the development of biological diversity and complexity over very long periods of time, (4) Once evolution got under way no special supernatural intervention was required, (5) Humans are part of this process, sharing a common ancestor with the great apes,

    Obviously, I agree with all of this. Of course there’s no need to say “evolution ‘and’ natural selection”, natural selection is one part of evolution. I’m sure that trivial mistake was not Collins’ own.

    (6) But humans are also unique in ways that defy evolutionary explanation and point to our spiritual nature. This includes the existence of the Moral Law (the knowledge of right and wrong) and the search for God that characterizes all human cultures throughout history.

    My main problem is with “that ‘defy’ evolutionary explanation”, of course, since I don’t personally agree that ethics or the search for God by humans necessarily “defy” evolutionary explanation. I’m also not sure all other animals entirely lack traits that are somewhat analogous to human “morality”.

    If it weren’t for that annoying and familiar bit about the “improbability” of the universe, which ironically would have no “spiritual” implications one way or the other, I’d think the last bit about human uniqueness (which appears to be the original part) to be very mild and probably non-disprovable. As I mentioned above, for whatever reason, that “improbability” thing seems to have weird appeal to otherwise highly functional people.

    I continue to see Francis Collins as an example of a highly productive scientist who follows a traditional religion, and I’ll probably use him as an example as such in the future. My admiration for his scientific achievements far outweighs my disapproval of his subtle but uneniable ventures into anthropomorphism and teleology. However, future mentions will come with caveats.

  46. #46 harold
    August 2, 2007

    I capitalized “God” because I was referring to what someone else wrote about Collins’ views.

    I don’t believe in an anthropomorphic god, nor care one way or the other whether that word is capitalized.

    Not that it makes any difference; I’ve just noticed that some people get triggered when they see that word capitalized (which I think is a bit pedantic). You can imagine a lower case “g” if it makes you feel better.

  47. #47 Torbjörn Larsson, OM
    August 4, 2007

    harold:

    Since we’re already here, and looking back, we cannot possibly see anything other than a history of a universe which is suited to the emergence of human life.

    Hmm. That was the best formulation I’ve seen on how to avoid the usual mistake of confusing a priori probability with a posteriori outcome.

    And yes, Collins on morality is not agreeable with biologists who looks on altruism and kinship relations.

    I’ve just noticed that some people get triggered when they see that word capitalized (which I think is a bit pedantic).

    In my case it is also a reaction to english usage of capitalization – I’m used to it for names of persons and geography only, so it seems like a personalization and honorific. For example, not all christians believe in a personal god.

    But generally I think it is because individuals of different world views recognizes (or not) none, one, or several gods, all different from each other. So it seems funny and/or impolite to confuse them with each other, and to confuse them with the general concept.

    It must make analysis harder as well for those who use this convention. I don’t notice it any more, it is like those religious texts that can haphazardly be quoted in the middle of some discussions, they are just bypassed like getting used to the sounds of Tourette sufferers.

  48. #48 Torbjörn Larsson, OM
    August 4, 2007

    harold:

    Since we’re already here, and looking back, we cannot possibly see anything other than a history of a universe which is suited to the emergence of human life.

    Hmm. That was the best formulation I’ve seen on how to avoid the usual mistake of confusing a priori probability with a posteriori outcome.

    And yes, Collins on morality is not agreeable with biologists who looks on altruism and kinship relations.

    I’ve just noticed that some people get triggered when they see that word capitalized (which I think is a bit pedantic).

    In my case it is also a reaction to english usage of capitalization – I’m used to it for names of persons and geography only, so it seems like a personalization and honorific. For example, not all christians believe in a personal god.

    But generally I think it is because individuals of different world views recognizes (or not) none, one, or several gods, all different from each other. So it seems funny and/or impolite to confuse them with each other, and to confuse them with the general concept.

    It must make analysis harder as well for those who use this convention. I don’t notice it any more, it is like those religious texts that can haphazardly be quoted in the middle of some discussions, they are just bypassed like getting used to the sounds of Tourette sufferers.

  49. #49 David Marjanovi?, OM
    October 28, 2007

    Beautiful.

    So 10 or 20 tentacles are the normal state for (…crown-group…) cephalopods… and Nautilus adds completely neomorphic tentacles… cool.

    James Collins above hasn’t noticed that molecular phylogenetics is neither done by comparing genome sizes nor by comparing gene numbers. It is done by selecting genes that evolve at appropriate speeds and looking for innovations in their sequences that are shared between species.

  50. #50 David Marjanovi?, OM
    October 28, 2007

    Beautiful.

    So 10 or 20 tentacles are the normal state for (…crown-group…) cephalopods… and Nautilus adds completely neomorphic tentacles… cool.

    James Collins above hasn’t noticed that molecular phylogenetics is neither done by comparing genome sizes nor by comparing gene numbers. It is done by selecting genes that evolve at appropriate speeds and looking for innovations in their sequences that are shared between species.

  51. #51 Lago
    October 28, 2007

    “”This type of logic is common throughout the flaky theory of evolution. Using the logic of this author we could ‘safely’ assume that a platypus is closely related to a duck, which is an absurdity of course.””

    So, you think it is equal to say, a structure, which has a totally different embryonic origin, and is made up of different parts based on comparing to the common vertebrate gnathostome plan, and is different both histologically and biochemically from one another, yet, due to a great reduction in teeth in both (done in very different ways ontologically speaking) and one having a similar general shape to the other based on the observational level of a 5 year old, we can call this equivalent to the deeply held similarities between a modern ape and a human where these similarities are on ALL levels and in the upper 90 percentiles?

    Does one really need to go into the vast details that support just how absurd your statement is?

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