Pharyngula

The platypus genome

Blogging on Peer-Reviewed Research

Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.

We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.

Let’s start with the first figure from the paper, a cladogram illustrating the sequence of appearance of derived traits in the relevant lineages examined in this work. This is a fairly conventional picture of our evolutionary history, and I have to emphasize that this paper reinforces the evolutionary explanation for the illustrated relationships.

i-f7b090191e79f3c0f4ba4dc4f73d9b5b-monotreme_cladogram.jpg
(Click for larger image)

Emergence of traits along the mammalian lineage. Amniotes split into the sauropsids (leading to birds and reptiles) and synapsids (leading to mammal-like reptiles). These small early mammals developed hair, homeothermy and lactation (red lines). Monotremes diverged from the therian mammal lineage 166 Myr ago and developed a unique suite of characters (dark-red text). Therian mammals with common characters split into marsupials and eutherians around 148 Myr ago2 (dark-red text). Geological eras and periods with relative times (Myr ago) are indicated on the left. Mammal lineages are in red; diapsid reptiles, shown as archosaurs (birds, crocodilians and dinosaurs), are in blue; and lepidosaurs (snakes, lizards and relatives) are in green.

Note that the study includes genomic data from the chicken; it is not implying that monotremes are part bird. Birds are used as contemporary representatives of the sauropsid lineage, a group of reptiles that split off our family tree 315 million years ago. They are distant cousins. What’s useful about their comparison is that, for instance, if we find a feature in birds that is also present in monotremes, marsupials, or eutherians, it is likely that that feature was also present in our paleozoic common ancestor.

For instance, one of the unusual (for a mammal) features of the platypus is meroblastic cleavage. There is a famous telegram from 1884 sent from Australia to the British Association tersely announcing a dramatic discovery: “Monotremes oviparous, ovum meroblastic.” Those four words declare that the platypus and echidna are egg-layers (oviparous), and that the early stages of formation of the embryo resemble those of birds and reptiles, not mammals. We eutherians have eggs that go through holoblastic cleavage; the first cell divisions cut all the way through the ovum, producing multiple, separable daughter cells. In the meroblastic cleavage of the platypus and chicken, the large yolky egg would be inefficient to subdivide completely, so the early divisions are incomplete — they produce a sheet of cells on top of the large yolk that are cytoplasmically continuous with the yolk cytoplasm. This is a feature that is common in yolky eggs and is a consequence of physical constraints on cell division.

Now look at the cladogram. Birds (archosaurs) and lizards and snakes (lepidosaurs) exhibit meroblastic cleavage. Marsupials and eutherians divide holoblastically. To say that the platypus is part bird because of that is misleading; what we’d say instead is that meroblastic cleavage is likely to be a primitive character, one that was inherited from the last common ancestor of synapsids and sauropsids, over 300 million years ago. (Another possibility, of course, is that birds and monotremes evolved this feature independently, and it is an example of convergent evolution. Just the observation of one character is not sufficient to judge, and we have to look at multiple details of the process to determine whether something is a product of convergence vs. common descent.)

Every organism is going to be a mix of conserved, primitive characters and evolutionary novelties — a mouse is just as “weird” as a platypus from an evolutionary perspective, since each is the product of processes that promote divergence from a common ancestor, and each are equidistant from that ancestor. It’s just that we primates share more derived characters with a mouse than with a platypus, because we are more closely related, and the mix of characters in the mouse are more familiar to us.

OK, all clear on this? It’s just a peeve of mine; modern echidnas, elephants, and emus are all products of different evolutionary trajectories through history, and no one by itself is a representative of the ancestral condition. We derive the ancestral state by comparison of multiple lineages. And that is the virtue of this paper, that it adds another lineage to the data set, one that diverged from ours over 160 million years ago. It is a lens that helps us see what novelties arose in that 160 million year window … on both the eutherian and monotreme sides.

So what are the details that we’ve learned from the platypus?

One important message is the unity of life. The platypus has about 18,000 genes; humans have 18-20,000 genes. Roughly 82% of the platypus genes are shared between monotremes, marsupials, eutherians, birds, and reptiles. This is not at all surprising. All of these organisms are made of eukaryotic cells, and the basic eukaryotic machinery is going to be shared. We also share a lot of junk: about half the platypus genome consists of LINE and SINE-like sequences.

We do differ in the details. For instance, an obvious difference is that the platypus lays yolky eggs, while eutherians have yolkless eggs retained in the mother. As you might expect, the platypus has a gene that we lack, for vitellogenin, a crucial yolk protein.

Something that eutherians and monotremes have in common, but which is not shared with birds, is lactation (some birds can produce crop milk, but this is a different adaptation). In the ancestral state, lactation was probably the secretion of fluids and immune system proteins to keep eggs and newborns hydrated and protected, but in our history, parents who invested more effort in secreting additional nutritive components, like sugars, fats, proteins, and calcium, were more successful. The platypus secretes a true milk, loaded with all of those goodies. One of the predominant proteins in milk is a phosphoprotein called casein, which is thought to have originated by a duplication of a tooth enamel matrix protein gene, of all things. These tooth genes, enamelin and ameloblastin, are clustered with the casein genes in both platypus and the mouse, suggesting that the kind of sophisticated lactation abilities we share arose prior to the Jurassic.

One of the hotspots for adaptive change in all organisms is the immune system, since every organism has to face ongoing challenges from viruses and bacteria throughout its life. One of the advantages of being a placental mammal is that our embryos, which have poorly developed immune systems, can benefit from a prolonged period under the umbrella of the adult, maternal immune system, something an egg-layer lacks. The platypus genome has a large expansion of natural killer receptor proteins, certain antimicrobial peptides, and other components of the innate immune system.

An interesting specialization in the platypus is the evolution of venoms. The platypus has small, sharp spurs on its hindlimbs that it uses to inject defensive poisons into predators, a very unusual feature not found in other mammals. Where did these venoms come from? As it turns out, by duplication of genes that have other functions, with subsequent divergence, and many of these genes also come from the innate immune system. In particular, there are a set of proteins called the β-defensins, which we also have, as do plants, fungi, and invertebrates. These are small, cystein rich peptides that are rather like the bullets of the immune system; they can bind to viral coat proteins, they can punch holes in bacterial membranes, and we have many epithelial cells that secrete these onto our skins and the lining of our gut and respiratory tract to kill invaders. Cells of the immune system spew these onto foreign and phagocytized cells to kill them, too. The platypus has repurposed these genes, making copies that have been selected for more effective toxicity when injected into other animals.

One very cool observation is that these are also the same proteins used in venomous reptiles — snake venoms also contain novel forms of β-defensins. So, on our cladogram, two distant relatives, the lepidosaurs and the monotremes, all use β-defensin derived venoms. Does this imply that their last common ancestor also used these venoms?

No, and this is where the details are important. Venomous snakes and the platypus have different duplications of the β-defensin genes. So, while coopting these immune system proteins seems to be a common strategy for evolving venoms, the details of the duplications reveal that these are independently derived features, not primitive at all. This is clearly a case of convergent evolution.

i-e2bf909419afecb43aad48d9388115df-defensins.jpg
(Click for larger image)

The evolution of β-defensin peptides in platypus venom gland. The diagram illustrates separate gene duplications in different parts of the phylogeny for platypus venom defensin-like peptides (vDLPs), for lizard venom crotamine-like peptides (vCLPs) and for snake venom crotamines. These venom proteins have thus been co-opted from pre-existing non-toxin homologues independently in platypus and in lizards and snakes.

i-f239c8923d353dcfad8fb5bd48d297f0-genome_status.jpg

The accompanying news article in Nature has a diagram that puts this work into context, showing the status of various ongoing genome projects. The first thing you should notice is that they are really heavily emphasizing mammalian genomes. I think this is justifiable; for puzzling out the significance of differences in the genomes, a good cluster of closely related species would have some real advantages in simplifying the problem. That the clade chosen happens to be mammalian is not quite as defensible on scientific grounds, but is a reasonable choice on economic and medical grounds, and also on the very important criterion of human vanity.

One virtue of the platypus is that it provides a relatively closely related outgroup to help tie together, and give perspective on, the various mammalian genome projects. It’s all part of the big picture in defining what a mammal is.

Of course, what we also need is an equally heavy investment in other diverse clades, like the molluscs (they aren’t on this figure at all!), the arthropods (only three species? Pathetic), protists, and bacteria (which are diverse enough to swallow everything else). Actually, we have to face the facts: what we really need are the complete genomes of every species on earth in a nice database where we can compare everything.


Brown S (2008) Top billing for platypus at end of evolution tree. Nature 453(7192): 138.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Ole Kriegs J, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453(7192):175-183.

Comments

  1. #1 Mustafa Mond, FCD
    May 10, 2008

    Here’s a great article on it:

    Neither fish nor fowl: Platypus genome decoded
    by Marlowe Hood
    …the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal.
    …missing link
    …The bird-like qualities implied by its Latin name, Ornithorhynchus anatinus, include webbed feet, a flat bill similar to a duck’s…

  2. #2 Don
    May 10, 2008

    Can we at least say that the platypus is a good argument against intelligent design? It looks bleeding ridiculous; the designer must have been smoking crack to make something like that.

  3. #3 MIkeG
    May 10, 2008

    Thanks for this. The news commentary was bugging me, too.

    And wow, that’s a hell of an author list.

  4. #4 Rusty
    May 10, 2008

    “Genome analysis”? Wizardry!

  5. #5 PZ Myers
    May 10, 2008

    Errm, that’s the very first link in my article, and I’m criticizing that dreck.

    And no, we can’t say the platypus is an argument against ID because it looks ridiculous. We look equally ridiculous. It’s an argument ID because it has features that show signs of its history, just as we do.

  6. #6 PatrickHenry
    May 10, 2008

    I suspect that if the platypus were found only in the fossil record, it would be described as a great example of a transitional fossil — maybe one of the best such examples. The fact that it’s survived all these years shouldn’t diminish its clearly transitional nature.

  7. #7 Karen
    May 10, 2008

    Yay, cladistics!

  8. #8 Bill Anderson
    May 10, 2008

    This is a great post! Be sure to include this topic in your book.

  9. #9 Milo Johnson
    May 10, 2008

    I’ve been hoping all week that you would write on this, thanks very much!

  10. #10 MikeK
    May 10, 2008

    All extant life forms are transitional, unless they become extinct. Transitional to what is the question?

  11. #12 Ted D
    May 10, 2008

    What can one say but: cool!

    Even makes me pine for that cladistics course I took. How something can be so fascinating and dull at the same time I’ll never figure out. This platypus thing is all fascinating though.

  12. #13 Richard Harris
    May 10, 2008

    I thought that it was ridiculous to say that the platypus was part bird. Who the heck is allowed to write that kind of crap for a science website? As PZ says, it is more reasonable to say that it’s part reptile.

    With such ignorance, it’s little wonder that Creationism flourishes amongst the deluded bible-bashers.

  13. #14 Bob O'H
    May 10, 2008

    I think the reason protists and bacteria aren’t on that figure is because it’s only showing animals. For example, yeast, rice and the weed (thale cress) are missing. According to wiki, several protists have already been sequenced.

  14. #15 Longtime Lurker
    May 10, 2008

    Thank you, professor, for cutting through the “woo”.

    Concise, easy to comprehend for a layperson with a genuine desire to learn, now THIS is science writing. The general quality of “science journalism” is really piss-poor. Maybe an op-ed delineating the proper way to report about scientific topics is in order, dear sage.

    Has anyone ever seen a cladogram printed in the science section of a newspaper at any time? Now, that would be invaluable.

    Hey, does anyone think that any of our resident trolls (hi Kenny!) will comment on this post?

  15. #16 Monado, FCD
    May 10, 2008

    The platypus is just as well-suited to its streams and way of life as the otter is to its.

    One article I read said that the platypus has a beak like a duck! What nonsense! A duck has a hard, horny beak. A platypus has a soft, leathery beak full of sensitive nerve endings. They evolved separately and the resemblance is superficial. Grrr!

  16. #17 Burt Humburg
    May 10, 2008

    I, too, have been hoping for a Pharngulaic takedown of the “platypi are reptiles, birds, and mammals” crap that came out this week. Unfortunately, you’ve been busy grading. And writing your book.

    So when are you retiring from teaching? Or are you going to do a Gouldian thing? (Do people come in from the community to audit your courses?)

    BCH

  17. #18 Kagehi
    May 10, 2008

    One article I read said that the platypus has a beak like a duck! What nonsense! … They evolved separately and the resemblance is superficial.

    I am reminded of the tale of three blind men and an elephant. lol

  18. #19 Alex
    May 10, 2008

    I have to put in a word for the Bacteria and Archaea. According to the NCBI Microbial Genomes webpage, there are almost 700 sequenced Bacterial and Archaeal genomes. Because they have smaller genomes with fewer sequencing complications, Bacteria and Archaea are the low-hanging fruit of the genomic world. Granted, those 700 sequenced genomes represent only about 300 “genera” (the term isn’t especially meaningful in Bacteria and Archaea), and it would be nice if there were more than 60 Archaea represented. Nonetheless, all these genomes have given us lots of insights into diversification, genome dynamics, and so on. The fact that we have coverage of such diversity (from Acidivorax to Zymomonas) and also of such fine scale (34 different strains of E. coli) is letting us see evolution on a large and a small scale.

    But none of them is as cute as a platypus or squid, so most people don’t notice.

  19. #20 Dave Carlson
    May 10, 2008

    Ah, how I miss these kinds of posts! More, please! :)

  20. #21 Rey Fox
    May 10, 2008

    Placental the sister of her brother Marsupial
    Their cousin called Monotreme, dead uncle Allotheria

  21. #22 Mike Haubrich, FCD
    May 10, 2008

    I think that what you have written is a great illustration of how genetics and expression are entwined in the tangled bank. Of particular interest to me is the relationship between the immune system of mammals and the venom of lizards and snakes.

    Of course, the creationist will say that this is an example of “front-loading” by the designer.

    And for the creationist position on the platypus (in finer detail) I bring attention to this article in Answers in Genesis from 2002:

    Scientists initially considered the platypus to be ‘primitive’, but then they discovered the incredibly complex electrolocation techniques the animal uses to find food. To evolutionists this made it a ‘highly evolved animal and not a primitive transition between reptiles and mammals.

    (snip)

    In reality, there is nothing in the fossil record to indicate that the platypus was ever anything other than a platypus. It is not a living ‘transitional’ form. It is a truly unique creature, and one that continues to baffle those who insist on making it fit into an evolutionary tree.

    If the understanding of evolution depended solely on the fossil record, she may have a partial case for her conclusion, but the sequencing of the platypus shows yet again how the fossil record and genetics complement, rather than compete against, each other.

  22. #23 Peter Ashby
    May 10, 2008

    You can see where the part bird bit comes in. The paper compares them to the chook genome AND they have a BILL, like a duck. It is therefore a no brainer for a journo, it is after all obvious that they are part bird, they are Duck-Billed after all.

    That the bill, including those sensitive touch and electroreceptors is clearly a newly derived feature that just happens to superfiically resemble a duck’s beak. The closest creatures to a platypus with electroreception are fish, a very few have extended it from the lateral line system. Elephant fish from Africa kept as aquarium specimens are an example.

  23. #24 FishyFred
    May 10, 2008

    What’s with naming dozens of authors on the paper?

  24. #25 Matt
    May 10, 2008

    That genome list seems woefully incomplete — where’s the doughty stickleback, the multiple Drosophila species, at the very least? I’m pretty sure there are a number of non-vert chordates in progress as well.

  25. #26 razib
    May 10, 2008

    Actually, we have to face the facts: what we really need are the complete genomes of every species on earth in a nice database where we can compare everything.

    christ. i thought you didn’t believe in god….

  26. #27 tristero
    May 10, 2008

    One more wonderful post in which a genuinely complicated subject is explained in a way that is both comprehensible to this layperson AND retains the sense that the subject is subtle and intricate. This is important, as a lot of science writing for laypeople gives the false impression that, after reading it, we can talk knowledgeably about deep subjects, like quantum physics, when in fact, we can’t.

    It’s also important because it whets our appetite to learn more about a topic.

  27. #28 Cuttlefish, OM
    May 10, 2008

    The genome of the platypus,
    We read today in Nature,
    Befits a beast so odd it once
    Defied our nomenclature;
    A mammal, but it still lays eggs,
    And you know what that means:
    The platypus and lizards share
    Some families of genes!
    Although the tale is quite complex–
    A long way off from solved–
    The genome of the platypus
    Shows how we all evolved!

    http://digitalcuttlefish.blogspot.com/2008/05/its-reptile-its-mammal-its-super.html

  28. #29 James F
    May 10, 2008

    A Wordsworthesque wordsmith. Bravo!

  29. #30 Stanton
    May 10, 2008

    I suspect that if the platypus were found only in the fossil record, it would be described as a great example of a transitional fossil — maybe one of the best such examples. The fact that it’s survived all these years shouldn’t diminish its clearly transitional nature.

    There are at least two fossil monotremes that are assumed to be ancestral to the modern platypus, the first being the poorly known Steropodon of Lower Cretaceous Australia, whose fossil toothed mandible suggests that the upper jaw was a beak very similar to the platypus’, and the extinct Obdurodon of South America and Australia, which resembled an otter-sized platypus with molars (in modern platypus, the molars are lost upon reaching adulthood).

    Also, Professor Myers, don’t shrews and solenodons also have their own venom system?

  30. #31 James F
    May 10, 2008

    Placental the sister of her brother Marsupial
    Their cousin called Monotreme, dead uncle Allotheria

    Mammal, mammal
    Their names are called
    They raise a paw
    The bat, the cat
    Dolphin and dog
    Koala bear and hog
    The fox, the ox
    Giraffe and shrew
    Echidna, caribou

  31. #32 amphiox
    May 10, 2008

    This was a great post. I’m waiting for the creationists to pick up on the “related to birds” bit and try to spin that as evidence against common descent.

    Sadly, by the time we finish sequencing the genome of every living species on earth, some of them (hopefully not most of them) will probably be extinct. And some of them will be probably go extince before we even find out about them. Sigh.

  32. #33 Lago
    May 10, 2008

    OK, Monotremes show a lot of traits associated with a very long living branch (The longest actually) of mammalia known as Multituberculates. They were probably a side branch close to this group, but some have placed them within this group as well.

    This is pure ignorance:
    “…The bird-like qualities implied by its Latin name, Ornithorhynchus anatinus, include webbed feet, a flat bill similar to a duck’s…”

    These are not the “bird-like” traits in question, as those traits in monotremes are only superficially like a duck and are in fact greatly different and not bird-like at all. What is bird-like is the survival of certain genes that were found in the root vertebrate source (basically the basal amnoites) that was inherited by many lines, but lost in many as well. The fact that they are retained in birds as well as monotremes is just shit luck.

    There are several other genetic traits found as well that were probably common to a wide range of early amnoites that were later lost in many separate lines, including placental mammals.

  33. #34 Katharine
    May 10, 2008

    Say it with me now:

    CONVERGENT EVOLUTION.

  34. #35 plonkerinn
    May 10, 2008

    Sigh, I dont suppose either of those Nature articles have been made available online?

  35. #36 Mindcore
    May 10, 2008

    Got it, not a chimera.

    How about those poisonous spurs, thats hot!

  36. #37 CanadianChick
    May 10, 2008

    excellent post – I learned a whole bunch of stuff I didn’t know…I love the way you explain these things, PZ.

    and Cuttlefish? That was awesome.

  37. #38 Peter Ashby
    May 10, 2008

    There are that many authors on the paper because to leave one of them off would have been to denigrate their contribution. You get on a paper (or should only) when you contribute something original to it. So technicians often only get thanked. You can get on a paper by just doing analysis, statisticians get on that way for eg. To leave somebody off then would be a terrible thing.

    The genome sequence of anything is a huge undertaking, comparing it to other genomes and making sense of those comparisons is not trivial either. So I say celebrate all those names, for they deserve to be there.

  38. #39 LARA
    May 10, 2008

    Thanks! All this cool, clarifying knowledge and for free too! So now that we know the platypus is a not really a glued together beaver-duck genetically speaking, when you have more time could you maybe explain how the heck all ten of it’s sex chromosomes manage to line up in alternating sequence during meosis and still manage to go exactly where they are supposed to?

  39. #40 Aaron Golas
    May 10, 2008

    I just happen to be wearing my Das Actionkino Schnabeltier t-shirt today in solidarity.

  40. #41 heather
    May 10, 2008

    Thanks for the article – just in time for my lectures on vertebrates next week! I’m looking forward to clearing up a few misconceptions about platypus/reptile/bird relationships. By the way, what is the plural of “platypus”?

  41. #42 Vaughn
    May 10, 2008

    There are more ongoing genome projects than those few listed in the Nature News article. The Genomes On-Line Database lists eight on-going mollusc genome projects amongst the 936 “Eukaryotic Ongoing Genomes”.

  42. #43 Lago
    May 10, 2008

    “How about those poisonous spurs, thats hot!”

    OK, this spur was common knowledge about platypuses for a long time. What I guess is not so common knowledge is the fact that quite a few extinct mammals from the Mesozoic showed spines that may have been used in a similar way. In other words, at one time, small poisonous mammals were commonplace.

  43. #44 Lynnai
    May 10, 2008

    What irks me is the constant semi-search for or refferances to primitive creaturs, something that hasn’t evolved for millenia but is still alive that we can somehow use as proof of evolution.

    Ummm….. am I wrong in thinking that becuase evolution does work that that creature does not exist? (unless it is one sigular creature that has been alive that long.)

  44. #45 MIkeG
    May 10, 2008

    I have a bit of a technical question, maybe someone here can help me out.
    In a multi-gene phylogenetic analysis like this seems to be (I haven’t read the paper, yet. Waiting on interlibrary loan.) is there a way to analyze the data in a combined way? What I mean is do they use presence/absence (or brokenness) of genes as traits like the “old school” cladists in combination with the differences in the sequence of the genes in question?

    If so, how would you weight the presence/absence (or brokenness) of genes, versus the sequence differences? And I guess gene duplication and all that would further complicate things.

    This study must have used a hell of a lot of processor time, especially if they used Maximum Likelihood.
    I hope this question isn’t too unclear.

  45. #46 D
    May 10, 2008

    Wow… hooray for science and the internet!

    My friend and I were discussing the platypus just the other night, so it’s wonderful to see this development in the news. Before the internet, we could have spent days in a library trying to track this down – and we live by three universities, each with their own library, and there are another two public libraries around to boot!

    Excellent writing, Doctor Myers! This is how popular science ought to be done.

  46. #47 raven
    May 10, 2008

    What irks me is the constant semi-search for or refferances to primitive creaturs, something that hasn’t evolved for millenia but is still alive that we can somehow use as proof of evolution.

    We see this more often in plants. Redwoods, Metasequoia (dawn Redwood), gingko, equisetom, etc..are known from the fossil records and go way back.

    Australian living fossil pine:

    Wollemi Pine is believed to exist in only one location which is within 200 km of the heart of
    Sydney, Australia’s largest city. There are less than 40 trees. This makes it one of the rarest
    plants in the world.
    It belongs in the plant family Araucariaceae but has distinctive features.
    However it has very from any known living pine. Its closest relatives are probably the extinct pines which were a dominant feature of the landscape of what is now Australia during the Jurassic and Cretaceous Periods – between 200 and 65 million years ago. These pines are known to us only from fossils.

  47. #48 robbrown
    May 10, 2008

    Although I object to the article saying it is “part bird”, I think the gist of the article was pointing out that the line between mammals and reptiles is blurry, and here is an animal that more or less straddles that line. The more people are exposed to these blurry cases, the easier it is for them to accept evolution, in my opinion.

    I have to take issue with PZ’s comment that “We can say with equal justification that we are part reptile, too.” The word reptile is not generally used to represent a clade, but a paraphyletic group that specifically does not include mammals. Platypus, as I said, somewhat straddles that line (or is at least rather close to that line), while humans are much more solidly within mammal. I think “part reptile” is a reasonable way of expressing that.

  48. #49 Quidam
    May 10, 2008

    If you read Neil Shubin’s Inner Fish, you realize than we are ‘part’ a lot of things. Fish and reptiles are in our heritage, birds and platypussies are not. So it’s reasonable to say we (and platypussies) are part reptile, but not that we are part bird.

  49. #50 Betz
    May 10, 2008

    OT but at least a genome question: Assume some time in the future we know exactly what sections of the human genome are “junk”, i.e. we have the whole proteome figured out, etc.
    If you removed all the unnecessary stuff from DNA in some sort of homo superior experiment, would it make a difference? Would replication be faster and less prone to error, or conversely more so? Any macro effects that an organism would notice?

  50. #51 Katharine
    May 10, 2008

    Lynnai,

    You seem to be making the mistake that you and other creationists make so often:

    You are assuming platypi are right now as they were when they diverged into their own group of Monotremata, and you are assuming a similar pace of change among all species.

    Evolution works, retard.

  51. #52 Scott de B.
    May 10, 2008

    “What’s useful about their comparison is that, for instance, if we find a feature in birds that is also present in monotremes, marsupials, or eutherians, it is likely that that feature was also present in our paleozoic common ancestor.”

    This is what confuses me, because aren’t birds homeothermic? And weren’t some dinosaurs also homeothermic? Yet homeothermy on the chart above is listed only on the mammalian side. So is this convergent evolution or something inherited from the distant ancestor?

  52. #53 Sili
    May 10, 2008

    Ah! But can your fancy Science explain why platypodes are so adorable?!

    Thought not!

    “Who’s daddy’s favourite monotreme? – You are! Yes, you are, Snookums.”

  53. #54 Lago
    May 10, 2008

    Reptiles, to many, still represents the basal amnoite condition, which both synapsids and saurapsids were derived. Many people in the scientific community have decided to place reptilia in one branch alone (sauripsida), while most of us grew up thinking of the first egg laying animals as the very definition of reptilia.

    Scientists and lay-people alike will continue to refer to basal amnoites as reptiles for simplicity and to help remove confusion in the general public, and those that do not like this, can eat me…

  54. #55 Etha Williams
    May 10, 2008

    @#49 Betz –

    Assume some time in the future we know exactly what sections of the human genome are “junk”, i.e. we have the whole proteome figured out, etc.
    If you removed all the unnecessary stuff from DNA in some sort of homo superior experiment, would it make a difference? Would replication be faster and less prone to error, or conversely more so?

    There was actually a 2004 Nature paper addressing this question (MA Nobrega et al, 2004; publicly available here). They used targeted cre-lox recombination to generate mice heterozygous for large deletions in apparent junk dna and then performed an intercross; they found that the homozygous offspring were almost indistinguishable from their WT littermates:

    We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice.

    They hypothesize that the minor expression differences observed are due to presence of unidentified regulatory sequences in the supposedly junk DNA, and in fact identified one such sequence using a beta-gal reporter assay.

  55. #56 MIkeG
    May 10, 2008

    re: Betz @ 49,
    To add a hypothesis to Etha’s information, I would guess that a lot of the extra stuff either must be totally neutral, or slightly beneficial. If it were even slightly detrimental, it would have been pared down over the long haul of evolution. Maybe all of the extra junk serves as a bit of a buffer. Say polymerase makes a mistake every 1000 bases (random overestimate) that doesn’t get corrected, if every single base was either coding or otherwise necessary, those errors would become rather important. If, on the other hand, there are little stretched of nonsense that get cut out of an important gene (i.e. introns), then there’s the increased possibility that the error won’t matter, as it would be in the bit that’s cut out.

    At least that’s what they taught me before I decided to work with organisms that don’t bother with introns.

  56. #57 MIkeG
    May 10, 2008

    addendum: As for all the junk that isn’t spliced in the middle of genes, that last hypothesis of protection against copy errors won’t really work. But the hypothesis that it isn’t detrimental could be tested. We can insert junk into genomes without breaking genes or other functional areas to see if it does anything. I don’t know if that’s been done.

  57. #58 Lurker #753
    May 10, 2008

    @51 Katharine

    “Evolution works, retard.”

    WTF? You clarify a particular point (which lies in a standard creationist blindspot, so no surprise)….. and follow that with a quick size 12 to the groin.

    Yay for civilisation! Go team! With new “Ad Hominem Ad Newbiem(tm)” technology, we’re surely destined for greater things!

  58. #59 valor
    May 10, 2008

    OK, moderately off topic, but I have need for advice or information:

    It seems like my intro to biology course completely skimmed over (and by this I mean, didn’t mention) cladistics, and while I can sort of grasp the nature of it, I’d really like more in-depth knowledge. Is there a resource or a book or something that someone can recommend to me? I’d really appreciate it.

  59. #60 Bride of Shrek
    May 10, 2008

    I’ve got a big fat daddy one in the creek behind my house. I take the kids down to watch him in the mornings as he suns himself around the place. I do however teach them, as we were taught as kids, never try to touch the bloody things. They can have nasty tempers and the spurs on the males can be extremely painful if you’re barbed. I think I’m going to name this fella PZ in honour of our Evil Overlord (TM). They do have kinda the same facial hair :-)

  60. #61 MIkeG
    May 10, 2008

    Careful valor, those cladistics folks got their start in Germany. They over-engineer everything, even their science.

    A few googles about parsimony and cladistics and characters should start you down the road. I don’t have any books to recommend, as most of mine are out of date, not particularly readable and centered on genetics (with lots of equations and algorithms). Oddly enough, the wiki article isn’t too bad: Cladistics.

    Hope that helps.

  61. #62 MIkeG
    May 10, 2008

    Bride of Shrek, may I simply express my jealousy? I’ve never even seen one in a zoo.

  62. #63 mothra
    May 10, 2008

    Trivia: The reason that the common name of this beast is Platypus while the genus name is Ornithorhynchus is that in 1793, Herbst described the BEETLE genus Platypus, some 6 years before the description of the Platypus (mammal. The equally wonderful (in its own way, beetle) belongs to the subfamily Platypodinae, part of that most successful of all living eucaryote lineages, the weevils, Curculionidae. The Wiki entries on both ‘Platypuses’ have been out of date since their inception.

  63. #64 valor
    May 10, 2008

    Thanks, MIkeG

    That Wiki article does look helpful.

  64. #65 miller
    May 10, 2008

    Wait, wait, so the platypus *isn’t* the crocoduck? Evolution is left defenseless! ;)

  65. #66 Lynnai
    May 10, 2008

    “Lynnai,

    You seem to be making the mistake that you and other creationists make so often:

    You are assuming platypi are right now as they were when they diverged into their own group of Monotremata, and you are assuming a similar pace of change among all species.

    Evolution works, retard.”

    I typed quickly, and you you missread me, I think mutual fault is here.

    Of course evolution works, that was my point. My thought wasn’t even about platypi, my thought was about nature journalism trying to be sensational and like to make broad statements, my favourite is ‘living fossil’.

    No not all species evolve at the same rate but if they have some mechanisim for repopulation they do evolve. Probably even stomatalites have evolved somewhat by now (but I’m willing to accept that one as only a probably, those things are weird).

    Journalists and second rate nature documentaries like to focus on superficial similarites(*) gloss it over with poor writing (much along the lines of ‘part beave part duck’ only more like ‘throw back’ and ‘living fossil’) and propgate the same missunderstanding you are accusing me of. That is what I was part of what grumbling about complete with semi-rhetorical question at the end.

    I admit though, it’s been a long time since anyone agreed with me quite so obnoxiously.

    (*) To be more precise the study of different rates of evolution getting misinterpreted by said same as the search for a creature which has not evolved thus proving evolution. That very idea makes my head hurt with it’s relitively subtle twist of illogic.

  66. #67 TomG
    May 10, 2008

    @45 MIkeG

    In a multi-gene phylogenetic analysis like this seems to be (I haven’t read the paper, yet. Waiting on interlibrary loan.) is there a way to analyze the data in a combined way? What I mean is do they use presence/absence (or brokenness) of genes as traits like the “old school” cladists in combination with the differences in the sequence of the genes in question?

    Excellent question, but this paper isn’t a phylogenetic analysis. What they’re doing here is comparing aspects of the platypus genome to other vertebrate genomes.

    Multigene (really, multilocus) phylogenetics is becoming increasingly popular, and for good reason. Individual genes have their own tree that isn’t necessarily concordant with the species’ tree! A combination of genes can water down those effects. This is all within the purview of coalescent theory, which is a bit difficult to wrap one’s head around at first.

    Also, it is possible to code higher level aspects of the genome in a manner similar to the way one would code a morphological character (say, the presence or absence of poison spurs). The presence of certain transposable elements, for instance, can be coded as a single character if it appears to be phylogenetically informative.

    If so, how would you weight the presence/absence (or brokenness) of genes, versus the sequence differences? And I guess gene duplication and all that would further complicate things.

    Weighting is likely going to be arbitrary here, but is definitely necessary, otherwise the DNA sequence data would wash out the genome or morphological data by sheer magnitude. It’s possible to partition data sets by data type, too, which is less arbitrary.

  67. #68 Blind Squirrel FCD
    May 10, 2008

    MIkeG, I also envy Bride of Shrek her platypus.

    We had a fellow come to Minnesota from Down Under to teach Environmental (outdoor) ed. It took a lot of patient stroking to get him to walk through tall grass without flailing the ground ahead of him with a stout stick to drive away the venomous reptiles which he was sure were lurking there. Those Aussies seem to live in quivering fear of Nature. I suppose an only moderately venomous platypus must seem downright cuddly in comparison to the usual run of spiders, snakes, octopuses and sea jellies.

  68. #69 MIkeG
    May 10, 2008

    TomG thanks for the reply,
    Sorry for the multigene mistake, I should know better. I do tend to think in ORFs.

    OK, so doing phylogenetic analyses of genomes is a bit of a hybrid between the classic primitive/derived, presence/absence character analysis (like poison spurs) and the use of the gene sequences.

    Ideally, this is that marriage that cooler heads in the “gene v character” wars have been hoping for, yes? Once the genes/loci are understood and their interactions are better characterized they’ll carry more information than traits, since the traits may have more than one influencing gene. And again, development will have a huge impact, since a little tweak of expression may change traits.

    Oh! once the technology is there, gene expression throughout development may add huge resolution to closely related species, when used as traits (caveat: expression is easily tweakable, perhaps too much so). ‘Course, that can only be done with extant species.

    This is really cool shit.

  69. #70 sfs
    May 10, 2008

    MikeG@56
    The presence of junk can be mildly detrimental and still avoid removal by natural selection, provided the selection coefficient is weak enough. Animals generally, and mammals in particular, have fairly small effective population sizes (at least compared to organisms with more streamlined genomes), and therefore are more likely to accumulate mildly deleterious junk.

    Also, I don’t see how your buffer concept is supposed to work. Assuming the errors are randomly spaced, a gene of a fixed length will have the same probability of experiencing a mutation regardless of whether there is nearby nonfunctional DNA or not.

  70. #71 Rita Bennett
    May 10, 2008

    Bride of Shrek

    My salute to you. Pharyngula has many readers in many countries outside the USA. You do not comment thus:

    “The USA has stupid people, but where I live, we are all smart.”

    For anyone who has made a comment like this, it is getting tedious, because if you really look, you will find some in your country who think, for example, that Adnan Oktar, aka Harun Yahya is a genius.

    Christianity is not the only religion that has a creation myth.

    So, Bride of Shrek, thank you and blow a kiss to PZ the Platypus for me.

  71. #72 BadAunt
    May 10, 2008

    I remember reading that the platypus spends more time in REM sleep than any other creature. Since then my biggest question about the platypus is not ‘Why does it look so funny?’ but ‘What does it dream about?’

  72. #73 Betz
    May 10, 2008

    @ Etha Williams, MikeG, and sfs
    This longtime lurker thanks you all for the responses. I will have to check out that Nature paper; I can already predict much googling for vocab & concepts. Cool!

    Oh, and happy Mother’s Day(US) to you mothers out there – you know who you are. It might be just a greeting-card holiday, but at least it doesn’t have two months of religious jingles leading up to it.

  73. #74 Pierce R. Butler
    May 10, 2008

    … the very important criterion of human vanity.

    True Christians ™ excepted, as these are characteristically identified by their modest and ingratiating humility.

  74. #75 Richard
    May 11, 2008

    As an Aussie, I found this really fascinating. Much better than the way it was presented on the news (where they used the term ‘amalgam’). The popular media is a really bad source of info on evolution (think of how they hyped up Nebraska man and Archaeoraptor).

    Also remember on my Netscape homepage they had an article about those studies that showed how close T-rex and chickens are. They seemed to assume that it meant chickens are descended from T-rex! I thought it meant they shared a close common ancestor. A newspaper article on whale evolution said that it has been known since Darwin’s day that whales evolved from ungulates. Didn’t he originally propose that they evolved from Carnivora, and their ungulate affinities have only been worked out recently?

    I’d also like to point out how misleading the term ‘primitive’ is when applied to monotremes, when you consider how derived their morphology really is. Shrews, on the other hand, are, AFAIK, really quite conservative if you ignore their reproductive mode.

  75. #76 Joon
    May 11, 2008

    I find the ‘mammal-like reptile’ tag on the cladogram to be confusing and inaccurate. Rar.

  76. #77 harold
    May 11, 2008
    Here’s a great article on it:

    Errm, that’s the very first link in my article, and I’m criticizing that dreck.

    This particular article has been taken to the cleaners, and to some degree rightfully so, but at the same time, I think a bit of understanding may be in order.

    The truth is between “great” and “drek”.

    Platypi do superficially appear to share characteristics with ducks. They do have webbed feet, they do have similar looking “bills”. They do lay eggs. An association between platypi and ducks is embedded in popular culture, for better or for worse.

    A truly great article would have said “despite superficial resemblances, platypi are no more related to ducks than other mammals…”

    But the author did get quite a bit right as well, and failed only to rid herself of common subjective biases. Creationism is drek. This was solid mediocrity, and to be honest, it would have taken only a bit more effort to make it genuinely great.

    What irks me is the constant semi-search for or refferances to primitive creaturs, something that hasn’t evolved for millenia but is still alive that we can somehow use as proof of evolution.

    Ummm….. am I wrong in thinking that becuase evolution does work that that creature does not exist? (unless it is one sigular creature that has been alive that long.)

    In addition to the plant examples, there are many animal species with basic morphologies that have been present on earth for extremely long periods of time, mainly invertebrates. These lineages are just as evolved as more recent ones, but in these cases evolution has conserved basic body plans in more detail. Obviously, our evolution has conserved basic body plans as well, but with a bit more variation from the norms of the distant past.

    I would guess that prokaryotic morphologies have been conserved for extremely long periods of time in many cases, but definitive fossils are much more rare.

    Once PZ gets his database of the genome of every living species, which sounds funny now, but is probably what will happen (in a couple of hundred years, post-docs will be wailing that they can’t find a single new obscure species to sequence the genome of

  77. #78 harold
    May 11, 2008

    Oops, I forgot to finish that one.

    I meant to say that with enough genome sequencing, it may eventually become possible to easily associate genome sequence with likely morphology, and conversely, to guess from morphologic evidence about genomic features.

  78. #79 Lyle G
    May 11, 2008

    I once attended a creationist lecture. At the question session I said, ‘If different species are not related, are independently created, why to all vertebrates have iron based blood, no nickel or copper or chrome, in different environments? He replied, ‘That’s just good design.’ I said the platypus and ekidna, mammals with reptile type elimination and reproduction organs, Is that good design?’seemed to fluster him a bit. Perhaps I was unfair to the platypus.

  79. #80 Echidna
    May 11, 2008

    raven@48
    The Wollemi Pine is as you say. As an update, because it is so rare, the conservation strategy was to keep the location secret while new plants were grown and made commercially available to the public. So now, instead of 40 trees being vulnerable to rare-plant hunters, development, fire etc., this past summer I saw Wollemi pines available for sale at my local plant nursery.

  80. #81 efrique
    May 11, 2008

    “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”.

    This sort of nonsense always irritates me greatly. If the only thing you’ve ever seen is a picture or a stuffed animal I could almost understand it. But all you have to do is watch a live one for a little while and see how exquisitely evolution has shaped them for their environment. They don’t look like bits-and-pieces then, not at all; everything seems almost perfectly fitted to everything else, as you’d expect with an animal that hasn’t had to change terribly much in a long time.

    I also get annoyed at people who refer to the platupus’ mouth as a thing like a duck’s beak. Again, in a photo, it’s superficially similar. When you see one actually being used you realize it’s a very different thing indeed – it’s versatile and rubbery (I keep wanting to say “appendage”) and acts as a sensory organ as well as a mouth.

  81. #82 Hematite
    May 11, 2008

    Great stuff PZ! More science!

    A question. PZ wrote:

    Every organism is going to be a mix of conserved, primitive characters and evolutionary novelties — a mouse is just as “weird” as a platypus from an evolutionary perspective, since each is the product of processes that promote divergence from a common ancestor, and each are equidistant from that ancestor.

    Emphasis mine. Is this an oversimplification? Surely how ‘far’ a species is from their common ancestor depends on where selective pressure has pushed them during the intervening time. It seems plausible that some species could remain largely unchanged if their ecological niche is the same as the ancestral species, but a species which has occupied several different ecological niches during its subsequent evolution should have moved ‘further’ from ancestral form. I am assuming some nonspecific but sensible measure of genetic or phenotypic distance.

    To phrase it another way, each modern species should have encountered a similar number of random mutations since the ancestral form, but some species will have found more of these mutations to be beneficial, and hence will have preserved more of them.

  82. #83 Hematite
    May 11, 2008

    While we’re talking about Australia, don’t miss Australia – the confusing country. It’s almost certainly not by Douglas Adams.

  83. #84 Peter Ashby
    May 11, 2008

    Blind Squirrel I know of what you speak re Aussies and poisonous beastie paranoia. Take a naive Aussie walking in the NZ bush, they will quail and exclaim when you nonchalantly step over a log on the path without checking for taipans on the other side. Takes them years to get over it. No snakes in NZ, not even in the zoos lest one escape.

    A lecturer of mine told us once of when he was out hunting with a friend, I forget the quarry, but he was belting through a field with long grass with his friend after it figuring that their vibrations were warning enough when a few feet ahead of him a large snake ‘stood up’ through the grass to see what all the fuss was about. He entertainingly relates how he acted like a cartoon character running in space in his efforts to stop.

    Remember 9 of the 10 most venomous snakes live in Australia, don’t talk about the spiders, the stonefish, the blue ringed octopus, box jellyfish etc, etc. It isn’t safe to go for a swim, or a walk, or anywhere really. Little wonder they are paranoid.

    Couldn’t happen to a nicer bunch of people but.

  84. #85 Hematite
    May 11, 2008

    In Platypus sex chromosomes and basal-equals-primitive linked by TR Gregory in #11, I don’t understand the objection to this statement:

    As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved.

    …which is compared to the allegedly obviously ridiculous statement:

    As the most basal mammal group, the duck-billed platypus is ideal for determining how the therian feeding system evolved.

    I think he is complaining that the platypus’s egg laying is implied to be the ancestral form, but that doesn’t seem pernicious except to mislead a poorly informed reader. What am I missing?

    Also, as a New Zealander it’s quite jarring to hear the platypus referred to as ‘duck-billed’ all the time. ‘Round here it’s just a platypus, and a koala is just a koala. Koala bear you say? It’s not a bear! I’m sure there are some Aussies around here to back me up.

  85. #86 Jay Ballou
    May 11, 2008

    Here’s a great article on it: … a genetic potpourri …missing link

    Can we at least say that the platypus is a good argument against intelligent design? It looks bleeding ridiculous; the designer must have been smoking crack to make something like that.

    suspect that if the platypus were found only in the fossil record, it would be described as a great example of a transitional fossil — maybe one of the best such examples. The fact that it’s survived all these years shouldn’t diminish its clearly transitional nature.

    Yeesh, how can people who post here be so clueless about fundamental concepts, especially after this article spelled it out? Look at the damn diagram — the playtypus is no more “transitional” or “ridiculous” or “a potpourri” or a “missing link” than any other organism at year 0. There’s nothing intrinsically odd or interesting about it. It only holds interest because of its isolation among extant organisms on its branch. If there were as many species of monotremes as of the other branches, no one would be tempted to put forth these absurd characterizations.

  86. #87 Jay Ballou
    May 11, 2008

    You seem to be making the mistake that you and other creationistsYou are assuming…. Evolution works, retard

    Ah, the irony. What part of Lynnai’s “evolution does work” are you too retarded to comprehend, and why did you assume she is a creationist?

  87. #88 Wowbagger
    May 11, 2008

    I’m with you Hematite – I dislike ‘duck-billed’ as a prefix as much as I do ‘bear’ after koala.

    I’ve been lucky enough to see one in the wild, too; they’re amazing creatures, even by wacky Australian standards. The other monotreme, the echidna (or spiny anteater), doesn’t get as much attention from the rest of the world ’cause it’s just thought of as ‘our’ equivalent of a hedgehog or porcupine. There’s nothing else in the world like a platypus – I wonder why Noah didn’t think it worthy enough of its own special mention…

  88. #89 Richard
    May 11, 2008

    Same here, Wowbagger. And just for the record, I don’t think most of my fellow Aussies are as paranoid of venomous creatures as people here have made us out to be. Most of us do not asct like Steve Erwin, either.

  89. #90 Nick Gotts
    May 11, 2008

    W.r.t. PZ’s comments on the phylogenetic distribution of sequenced species, has anyone given any serious thought to what strategy might be scientifically optimal, in the interim before every species is sequenced? Presumably it would depend on what you’re most interested in, but wouldn’t some kind of coordination be both possible and useful, so when a group of sequencers are selecting their next target, they take into account what other groups are planning?

  90. #91 Jay Ballou
    May 11, 2008

    here’s nothing else in the world like a platypus

    Only if the meaning of “like” is tailored just so as to make the statement true. But that sort of “like” makes it true of all sorts of things … including ducks, beavers, and humans.

  91. #92 Nan McIntyre
    May 11, 2008

    Enquiring minds have asked upthread about platypus’s plural.
    The word is a combination Greek word platy (broad) and pous (foot) – with the ending made into a bastardised Latin pus.
    This invites people to use the plural Latin ending – platypi – but the more strict usage would be – platypodes (as would be octopodes for the prof’s molluscan obsession).
    I’m in the anything’s ok camp with this burgered-up pretend-Latin nomenclature and platypoi, the strict Greek ending, is just as good for communication.

    I favour platypuses.
    Some go the most parsimonious route with a plain fishy platypus.

  92. #93 Ichthyic
    May 11, 2008

    Some go the most parsimonious route with a plain fishy platypus.

    *raises hand*

    same with octopus being the plural of octopus.

    just to add another level, when speaking of a group of different species, the ichthyologists I know tend to pluralize fish as fishes.

    fortunately, there’s only one species of platypus.

  93. #94 Wowbagger
    May 11, 2008

    Richard #89: it can sound a bit daunting when statistics like ’9 of the 10 most venomous snakes are found in Australia’ get thrown around but you have to be unlucky to come across any of them. It’s not like the whole country is wall-to-wall deadly creatures – though i have had some interesting experiences with snakes while mountain biking.

    As much as I respected Steve Irwin for bringing more attention to Australian wildlife I wasn’t that big a fan of his methods. I’m old enough to remember some excellent documentary work by a man named Harry Butler; he was just as informative without being sensational about it. Our creatures should be exciting enough without having to make it over-the-top.

    Jay #91: I’m sorry if my statement sounded sweeping and dismissive, or counter to the aim of the post – if that’s what you were calling me on. Thanks to this site (and others like it) I’m in no doubt that humans have a lot more in common with the platypus than I ever imagined.

  94. #95 GTMoogle
    May 11, 2008

    I’m going to have to call out robbrown for subject comprehension failure.

    Platypus, as I said, somewhat straddles that line (or is at least rather close to that line), while humans are much more solidly within mammal. I think “part reptile” is a reasonable way of expressing that.

    No! Stop it with the human-centered bias! Mammal is yes/no, not a percentage. Just because our half of the branching is more populous doesn’t make us more mammal. You might as well say we’re less animal-like than beetles. It’s just nonsense!

  95. #97 raven
    May 11, 2008

    this past summer I saw Wollemi pines available for sale at my local plant nursery.

    They are also for sale in the USA and Canada.

    Not inexpensive, 100 USD for a small tree in a pot.

    Wollemi pine is definitely a species on the edge. One article I read said the genetic variability of the remnant population was zero, highly inbred.

    IIRC, they also had a hard time propagating the pine for conservation. Not sure if the for sale plants are clones, cuttings, or seedlings.

  96. #98 Nick Gotts
    May 11, 2008

    No! Stop it with the human-centered bias! Mammal is yes/no, not a percentage. Just because our half of the branching is more populous doesn’t make us more mammal. You might as well say we’re less animal-like than beetles. It’s just nonsense! GTMoogle

    Mammal is surely only yes/no because we don’t have all the proto-mammals around – if we did, any line we drew between mammals and non-mammals would be arbitrary. Also, it might be the case that monotremes have more primitive and fewer derived characteristics (genetic, morphological, behavioural, whatever) relative to our last common ancestor with them than therians – or indeed, vice versa, in which case it would make sense to say the branch with a smaller proportion of derived characteristics is nearer the “edge” of the mammal class. Thirdly, suppose an alien you were instructing in Holocene Earth biology asked to be shown (a) A typical mammal; (b) A typical animal. I’d show them (a) A eutherian, probably a rodent and (b) a beetle.

  97. #99 Philip Bruce Heywood
    May 11, 2008

    The zoology, genetics, diagrams and so on look o.k. to me , but I’m not qualified to advize in those areas. PZ’s unwritten assumption re. what the geologic record suggests about the unfolding of life, is manifestly impossible, and the (again, unwritten, but assumed) mechanisms by which evolution is proposed to have been brought about, are impossible.

    The geologic record is of clear-cut species, that filled a niche FOR WHICH THEY WERE SUITED. They neither struggled into existence, nor did they take time to develop variety. Here is a simple and not totally accurate analogy of the fossils’ story: You are driving a vehicle along a smooth, all-weather, dustless road. Rough, dusty/boggy conditions loom ahead. By the time you are far into the off-road conditions, your vehicle at some precise point has instantaneously developed better off-road characteristics – slightly altered wheel-base, somewhat stonger suspension, a slower gear, higher clearance, heavier tyres, ETC.. It is a new model. (The older model may continue on, into the new conditions: and, sometimes, weird offshoots and attempts that are sometimes difficult for the taxonomist to ‘nail’, as being new, or variations of old species, may arise.)

    The message of the geologic column is that pre-existing species do not struggle towards becoming new species over time (although it is very conceivable that the struggles of the older species did have some bearing on the form the new species took): species debouched here, fully developed, with all variety built in, with great vigour and often in astonishing profusion. They met the needs of the new era: they were not a product of the new era. So, the platypus enjoys Australia, now: it is not half-way to becoming a platypus after having lived for millions of years in the conditions it now enjoys.

    The geologic record rules out natural selection and survival of the fittest operating over vast time spans, as an engine of speciation. It rules out common, or “blood” descent, just as logic and observation of the biosphere rule out common descent.

    The geologic column points clearly to environment as a trigger, acting on something like a set of options, so that the useful options tend to get employed, as soon as environment necessitates them.

    A set of options: if you like, a sort of a “mother board” setup. This permits the variety we see in the biosphere, whilst explaining why there is commonality. Evolution cannot lead just anywhere: even the platypus can be reduced to information components found in various classes: no animal is unique. Yet every animal is unique, because the information technology involved allows unique combinations of the finite number of options.

    We have looked into the species lock and various other considerations elsewhere.

    We are looking straight down the barrel of information technology and by logically following that path, we build a theoretical, fast becoming practical, picture, of what actually happens at speciation.

    HOX genes in paddlefish were waiting to be triggered somewhere down the path of evolution, so that animals could walk. They weren’t produced in paddlefish, through attempts at walking. Likewise, the basic “template” that was triggered into action to evidence the new features of new species, was not a product of the struggles of the new species. I’m not hereby defining how all those “templates” came to exist. It’s a large field, and rather new. I’m no I.T. man.

    Good old hoaxes such as ORNITHORYNCUS were suvivors of weirdo circumstances of time, location, environmental condition, and the evolutionary stage of the conduit forms that preceded them (- without being their progenitors). Evolution involved rather advanced genetic engineering, and at least quantum – category I.T..

    ORNITHORYNCUS was just one of the outcomes of information, playing on a finite array of ‘keys’, that brought forth music.

  98. #100 trrll
    May 11, 2008

    OT but at least a genome question: Assume some time in the future we know exactly what sections of the human genome are “junk”, i.e. we have the whole proteome figured out, etc.
    If you removed all the unnecessary stuff from DNA in some sort of homo superior experiment, would it make a difference? Would replication be faster and less prone to error, or conversely more so? Any macro effects that an organism would notice?

    By definition of “junk,” no. To put it another way, if removing a sequence produces any kind of effect “that an organism would notice” then it wasn’t junk to begin with.

    Presumably, replication would be faster, but replication does not seem to be rate-limiting in the growth of large organisms, and small organisms for which it likely is rate limiting don’t seem to have much in the way of junk.

    One might hypothesize that a population of organisms with the junk cleaned out might be slower to evolve in response to environmental challenges, since there would be less unpurposed genetic raw material for natural selection to work with, but this is pretty speculative. It would certainly be an interesting (but very difficult) experiment.

  99. #101 Etha Williams
    May 11, 2008

    @#93 Ichthyic –

    just to add another level, when speaking of a group of different species, the ichthyologists I know tend to pluralize fish as fishes.

    This is the same convention used when we say “peoples” (to describe a group of different cultures) — it’s the plural of a plural to describe a group of groups.

  100. #102 Nick Gotts
    May 11, 2008

    Philip Bruce Heywood – go and look up (a) The numerous observed instances of speciation; (b) the term “ring species”.

  101. #103 Hematite
    May 11, 2008

    Nick, I tried to have that conversation with PBH a couple of weeks ago – I don’t think you’ll get very far. Check the site he links to if you dare.

  102. #104 Katharine
    May 11, 2008

    Lynnai, Jay Ballou – I admit fault; to me, her first post read something like this:

    “The platypus is so genetically weird that I don’t see how evolution can work.”

    After seeing your subsequent explanation, I see that is not what you meant and that you aren’t saying evolution doesn’t work at all (to the contrary, you’re saying evolution does work, and I know evolution works too :) ).

  103. #105 robbrown
    May 11, 2008

    Mammal is yes/no, not a percentage.

    So are you suggesting that at some point in the past a “no” (i.e. non-mammal) gave birth to a “yes” (i.e. mammal)? That sure sounds like the sort of misunderstanding the creationists with their whole “kind” logic have.

    Seems to me that for several million years along the path from non-mammal-reptiles to mammals, there were animals that were “a percentage”. So that means the mammal clade, while monophyletic, still has a blurry edge, that potentially could remain blurry to the present day (if decendents of those “percentage” animals are still alive). Platypus may be considered fully within the mammal clade, but I still argue it is far closer to that blurry edge than we are.

  104. #106 Philip Bruce Heywood
    May 11, 2008

    Nick: Go and look the zoo. How many indisputably new species, the product of raw Nature as she exists without human intervention, come in every week? These new ‘species’ that we keep hearing about (especially since Darwin) are presumably 1) To do with that aspect of Nature that has been modified by the curse – viruses, harmful bacteria, various other pests. Some of these have gone genetically “tropo”: – constantly morphing, in a seeming conspiracy against higher life. 2) To do with life-forms that are all but impossible to perfectly categorize through observation, of which Darwin’s Finches are an instance: 3) To do with hybrids, new varieties/races, and such like, that either are temporary phenomena resulting from exceptional circumstances in Nature, or are engineered by Man. I am taking the definition of Species as that which historically is understood and established – ideally, reproductively self-contained units, found in Nature untouched by Man. What the average person gets the idea about, at zoos, in the farmyard, in Nature documentaries. They exist. Darwin wrote about them. Don’t be misled by hybridization. It is seldom, if ever, speciation: the existence of hybrids proves that genetically distinct and persistent units exist, enabling hybrids to be identified as such. As for some members of a species being unable to breed with other members, such as tiny dogs and large dogs: should this happen naturally – without Man – it could be a preparotary step towards speciation. As such, it would be superficial, in that isolation of itself doesn’t re-write DNA, immune systems, reproductive systems, nor trip species locks. But it could have meaning.

  105. #107 Stanton
    May 11, 2008

    Robbrown, just because a species or population is “closest to the ancestral form” does not necessarily mean that that species/population will look like the ancestral form. For instance, take kohlrabis, brusselsprouts, cabbage, broccoli and cauliflower. They are all descended from the same Mediterranean mustard plant, but, the kohlrabi is considered to be closest to the ancestral mustard species because the only thing that has been modified in the kohlrabi is the stem. But, it is totally impossible to mistake an adult kohlrabi for the ancestor.

    Likewise, just because the platypus (and echidnas) retain many important primitive characteristics (such as laying eggs, and lacking defined nipples) does not necessarily mean that the ancestral mammal looked like a platypus and or echidna. But, I think you know that already.

    Also, I like to think of classification as being akin to a Venn diagram/checklist, in that if a species or taxon displays certain specific traits, it can be placed within a bigger taxon, or placed near a bigger taxon, which is why we have “parareptile” versus “paramammal” versus “theraspid”

  106. #108 Nick Gotts
    May 11, 2008

    Philip,

    These new ‘species’ that we keep hearing about (especially since Darwin) are presumably 1) To do with that aspect of Nature that has been modified by the curse – viruses, harmful bacteria, various other pests. Some of these have gone genetically “tropo”: – constantly morphing, in a seeming conspiracy against higher life.

    This is just ludicrous religious verbiage – there is no “curse”, nor “conspiracy against higher life”. I don’t believe in your sky-fairy stories, so it’s just silly to bring them into an argument with me that is supposedly about scientific evidence and theory.

    Of course there are very many neatly distinct species – Homo sapiens being a good example. The point is there are many other cases where it is not possible to say definitively whether a collection of populations is one species or more than one – exactly what you would expect from the modern theory of evolution. Your claim that new species are not appearing is simply false. Moreover, there is clear evidence that in plants at least, hybridisation is an important mechanism of speciation – try looking up “autopolyploidy” and “allopolyploidy”.

  107. #109 Nick Gotts
    May 11, 2008

    Re #103 Hematite – Thanks; I thought the name was familiar! Still, at least his neo-Platonic battiness makes a change from the straightforward creobots!

  108. #110 robbrown
    May 11, 2008

    Robbrown, just because a species or population is “closest to the ancestral form” does not necessarily mean that that species/population will look like the ancestral form.

    Of course. My only point is that if the line leading to a modern species split off at a transitional point — where it is not clear whether it is fully mammal — by a cladistic view, the modern species would not be fully mammal either.

    Of course, categorization does tend to be based on currently extent species, so it is unlikely to have a living animal that doesn’t fit 100% in one category or another. When they found the platypus, they presumably had adjust the definition of mammal to fully include it, say by adding a clause that says that live birth isn’t an absolute requirement.

    But what if we happened to find a currently living animal in some remote place, whose common ancestor with modern therians lived some 50-100 million years before that of platypus? Mammal? or reptile? or would we just have to consider it “some percentage”? Whether or not it retains a similarity to that common ancestor, I think by a cladistic view we would have to consider it “partly mammal” in just the same way we would consider the common ancestor.

  109. #111 robbrown
    May 11, 2008

    Go and look the zoo. How many indisputably new species….come in every week?

    Go look at your fingernails. How often does a fingernail go from being indisputably short to indisputably long while you are looking at it?

    By your logic fingernails can’t go from being short to long, because no one has ever observed the exact moment when it happens.

    (I know, its pointless to try to convince this guy, but figured I’d practice my argument anyway….)

  110. #112 Andreas Johansson
    May 11, 2008

    It is therefore a no brainer for a journo, it is after all obvious that they are part bird, they are Duck-Billed after all.

    I spot a new angle for advancing my nefarious scheme to have Aves defined as the total group.

  111. #113 Nick F.
    May 11, 2008

    I don’t like the phylogeny figure from the Nature News article. Since when does evolution work in such a way that all the arrows point to humans? The tree too closely resembles one of Hennig’s ladders for my taste.

    I suppose that drawing the tree in what seems an anthropocetric manner could be useful if one wanted to convince the more human-health-oriented researchers of the importance of non-human genomes. However, this seems sloppy for a paper discussing evolution.

  112. #114 Philip Bruce Heywood
    May 11, 2008

    Nick says, “Your claim that new species are not appearing is simply false”. Robbrown, who seems to be genuinely trying to verbalize and visualize the process of evolution, says, “By your logic fingernails can’t go from being short to long, because no-one has ever observed the exact moment when it happens”.
    If speciation is happening, as Nick implies, why hasn’t anyone observed the fine detail, as Robbrown correctly implies?

    Robbrown, I invite you to analyze, verbalize, and rationalize, not only whatever theory you have been studying, but entries such as my two posts above, and my published site materials. Keep verbalizing and keep analyzing. Go on until there is no inherent contradiction.

    Nick, meanwhile, will tell us, rationally, how viruses got here. That’s after telling us at what stage, and how, and why, HOMO SAPIENS ceased interbreeding with its blood ancestor. Don’t bring in isolation: that won’t carry with the fossil record. Just like having one fish being the blood ancestor of another fish, doesn’t carry with the fossil record. The fossil record is one of evolution in the same locality, in the same ocean, on the same continent – often amongst species whose members are highly mobile.
    The hybridization aspect I shan’t pursue, as the literature pursues it for us. It is not regarded as the engine of speciation.

    Tell Rusty (Hematite) I’ve got something reseached on chops. Recently I had a big week, wrestling bears – decent bears, koala bears – and became very hungry. (I’d also been fencing, hand-digging post holes, and we got so far the first day, it took two days to get back.) Staggering to a serving board, I asked for chops. I was informed there was a choice in chops – AUS., N.Z., and U.S.. Being something of a patriot, I ordered the firstmentioned. A good choice it turned out to be, I might say. Impossible though it might seem, there remained a suggestion of hunger. By way of variety, I then ordered New Zealand chops. They took away the remnants of the Aus. chops, but I was surprised at how quickly they then served the other. But something about these chops looked familiar. I discovered that it was policy to serve the bones from Aus. chops, as N.Z. chops. So I then asked for U.S. chops. After a long delay, they dug out a box, with a bill of lading for the MAYFLOWER. It turned out that this box was also the one Washington was standing on in that row boat, when he crossed the Delaware on Christmas night, 1776, with such a way-out-there and forward looking pose. We now know he seemed to have his nose in the air for tangible reasons. He was, of course, contemplating the genome of sheep and goats, and wondering how a genome so similar accounted for them being separate species.

  113. #115 Alligator
    May 12, 2008

    Ever since freshman biology, I’ve been very troubled by the fact that the platypus does not have nipples. I’m ok with the duckbill, I’m ok with a mammal laying eggs — but seeping milk gives me the willies.

    Also, (despite my atheism) I’ve always loved the opening quote to Dogma : “Even God has a sense of humor. Just look at the platypus.”

  114. #116 shane
    May 12, 2008

    The Wollemi Pine is definitely available from nurseries in Sydney. Very cool moment seeing one for the first time as I hadn’t heard they’d been made commercial.

    I grew up in the country and one of my coolest memories is seeing a platypus on few occasions in the local creek. Probably only had the opportunity to see one in the wild since. Extremely shy creatures.

    As far as other dangerous creatures go. A healthy dose of paranoia is ingrained in you as a child especially if you grew up in the country. However the only person I personally know that was killed by a snake was our next door neighbours child and she was bitten by a snake in her backyard in town.

    In the bush we walk with our eyes down constantly scanning the grass or roads for that matter. Spend any time in the country you will almost step on a black or a brown or a tiger at some point. With a bit of luck they won’t snap at you (most of the time they’ll turn around and head back into the bush). We try not put our hands into logs or holes willy nilly. We had to be careful reaching for garden taps without looking. In the heat of the summer we’d occasionally have a big black snake wrapped around the tap. Going for dripping water I suppose?

    In some parts of Sydney you should check your shoes before you put them on in case of Funnel Web spiders. When we go swimming up north we try to avoid swimming in rivers that have large signs warning of crocs. Funny the number of tourists that think the signs are for local colour.

    Having said that you can’t be a bloody nervous nelly and be overly paranoid. We do have anti-venom available almost everywhere. I’ve been more paranoid in Africa or South America where I know that even if it is lowly number 20 on the list of most deadly (and most of the top 20 snakes are in Oz), I will still have more chance of karking it over there (Sth Am or Afr) because there will be NO anti-venom available.

  115. #117 arachnophilia
    May 12, 2008

    you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals.

    woah, hold on a second there. sauropsida, the group we tend to call “reptiles,” DOES NOT include eutherian mammals; synapsida DOES. the only clade that contains the platypus and lepidosaurs is amniota, which is not a “great reptilian clade” and so mammals are in no way “part reptile.” they are synapsid amniotes. your first diagram clearly shows this. though it’s worth noting that “mammal-like reptile” is misnomer that has sadly been retained just about everywhere for lack of a better term for non-mammal synapsids. for that matter, “reptile” itself is also a misnomer, for some of the reasons you just stated: it includes many groups that clearly do not fit the definition very well, including dinosaurs (including birds). still, “sauropsida” is the group with which we identify the term “reptile” and synapsids are technically outside of that group.

    but, yes, i agree. the article is dumb. they always are. my father (not a dumb man by any degree, especially not his ph.d.) mentioned to me the other day that they discovered the platypus was part bird through genetic analysis and my first response was a groan. “what, just because it has a bill?” i then, of course, proceeded to explain the evolutionary tree starting at amniotes, and detailed exactly how a platypus (or a human, for that matter) is related to a bird — sounds like yet another case of the press screwing up science reporting. further, i pointed out that this is not a suprise but rather a confirmed prediction of said cladistical analysis. the platypus retains a reproductive system more similar to a reptiles, so it should have some genes associated with that reproductive system in common with other animals that retain similar reproductive systems, like birds. good to know, but doesn’t make it “part bird.”

  116. #118 Ichthyic
    May 12, 2008

    This is just ludicrous religious verbiage

    don’t waste your time.

    having seen PBH post over on the thumb, it’s pretty clear he’s completely nuts.

    even worse than JAD.

    seriously.

  117. #119 G. Tingey
    May 12, 2008

    My sister-in-law lives in Tasmania, and she has at least one pair of Platypi living in the stream on her property.
    They aren’t “tame”, but if you sit, or move quietly, they will ignore humans. She does have pictures … but her cats are fascinated by the otter-analogues – which is what Platypi are.
    Their electric-field sensing around the duck-bill is incredibly good, which is how they detect their prey.

  118. #120 Michael Le Page
    May 12, 2008

    I’m glad you tackled this as the misleading coverage has been annoying me too, but you are completely wrong to blame journalists for it.

    Read the press releases that got sent out. Read the quotes provided by the leading scientists. Did the newspapers accurately reflect what they said?

    If yes, please do an update naming and shaming the real offenders.

  119. #121 Sven DiMilo
    May 12, 2008

    “sauropsida” is the group with which we identify the term “reptile”

    “We,” Kemosabe?

    When will knowledgable people stop trying to cram their cladistic monophyly fetish down the throats of ordinary folk who don’t give a shit? The dichotomy between “synapsida” and “sauropsida = reptilia” has only been clear for a couple of decades; for example, Pough’s 1989 3rd edition of Vertebrate Biology shows synapsids, testudomorphs (turtles), and diapsids as an unresolved trichotomy. In contrast, the colloquial (and, formerly, scientific) use of the word “reptile” to mean “amniotes other than birds and mammals)” dates back many centuries. Until the educational system ramps up to the point where Josephine off the street knows what a “synapsid” is, the term “mammal-like reptile” is both appropriate and communicative.
    Really, I’m all in favor of strict monophyly in formal taxonomy–I really am–but cladistic policing of informal and semi-formal language seems obnoxiously pedantic. See which gets the message across better: “Observe the non-ophidian squamate” or “hey, check out that lizard.”

  120. #122 arachnophilia
    May 12, 2008

    When will knowledgable people stop trying to cram their cladistic monophyly fetish down the throats of ordinary folk who don’t give a shit?

    pz myers doesn’t strike me as an “ordinary folk who doesn’t give a shit.” he strikes me as a person with a ph.d. in biology.

    and no, the distinction is not especially clear, is it? but that’s how evolution happens: on the species level. the first sauropsid and the first synapsid would only have been distinguishable by the placement of fenestrae in their skulls. their jaw structures would have both contained three bones, neither would have had mammary glands, and they both would have been cold blooded. looking at the first synapsid, your average person would have called it “a reptile.”

    but, if we’re complaining about colloquial misunderstandings of science, well… making an argument in favor of colloquial naming conventions is kind of silly, imho. i’m not trying to be pedantic about it, just accurate. calling mammals “part reptile” is technically incorrect, because mammals do not fall under monophyletic “reptile” clade. “closely related to reptiles” is fine. “very reptilian ancestry,” fine. but calling mammals “reptiles” would be wrong.

  121. #123 robbrown
    May 12, 2008

    pz myers doesn’t strike me as an “ordinary folk who doesn’t give a shit.” he strikes me as a person with a ph.d. in biology.

    Sven was clearly referring to PZ as one of the knowledgeable.

    And I agree with Sven….monophyletic clades are great for formal taxonomy, but I do not consider whales to be fish, birds to be dinosaurs, or humans to be apes. (whales ARE members of Osteichthyes, birds ARE members of Dinosauria, and humans ARE members of Hominoidea, however). Even whether humans are animals or not depends on the context.

  122. #124 arachnophilia
    May 12, 2008

    whales ARE members of Osteichthyes

    …no they’re not. whales are tetrapods (even if they don’t have four feet anymore), and tetrapoda and osteichthyes are sister clades, under gnathostomata. which, excluding tetrapods are still “fish” so i’m only making a minor correction here. last i heard “fish” is still considered paraphyletic and “reptile” was not.

    in any case, haven’t you heard “birds ARE dinosaurs” thrown around all over the internet? it’s practically the mantra of any practicing dinosaur paleontologist. the sentiment that human beings are great apes is similarly popular, if not quite as slogan-ized. the distinction is that these two are clearly monophyletic groups, and the example clearly fits the definition of the monophyletic group. and the specialization is not very extreme in either example. “whales are fish” is more of an in-joke. the evolutionary gap is clearly a much bigger one, and people find the convergence amusing. and, as i said, fishes are not monophyletic. “whales are fish” for the same reason that “people are fish.”

    that “reptile” should be replaced with a monophyletic sauropsida clade is a newer notion, yes, but only about as new as the notion that “birds ARE dinosaurs.” just not as popular, because dinosaurs are sexy. the two are actually somewhat related, because the classical definition of “reptile” would effectively exclude dinosaurs (birds), and make the group paraphyletic twice over by excluding mammals and at least a third of archosaurs, if not all of them.

  123. #125 Jay Ballou
    May 12, 2008

    Jay #91: I’m sorry if my statement sounded sweeping and dismissive, or counter to the aim of the post – if that’s what you were calling me on.

    I called you on being wrong, a wrongness based on selective perception and conceptual confusion.

  124. #126 David Marjanovi?, OM
    May 13, 2008

    There are at least two fossil monotremes that are assumed to be ancestral to the modern platypus,

    Be very, very, very careful with “ancestral”.

    Also, there are more fossil monotremes: Monotrematum from the Paleocene of South America, Teinolophos and Kollikodon from the late Early Cretaceous of Australia.

    the first being the poorly known Steropodon of Lower Cretaceous Australia, whose fossil toothed mandible suggests that the upper jaw was a beak very similar to the platypus’,

    Yep.

    and the extinct Obdurodon of South America and Australia, which resembled an otter-sized platypus with molars (in modern platypus, the molars are lost upon reaching adulthood).

    Yes, except it’s Miocene in age and didn’t occur in South America.

    Also, Professor Myers, don’t shrews and solenodons also have their own venom system?

    Yes, but those are totally different — their venom glands are modified salivary glands.

    OK, Monotremes show a lot of traits associated with a very long living branch (The longest actually) of mammalia known as Multituberculates. They were probably a side branch close to this group, but some have placed them within this group as well.

    Untrue, untrue, untrue, and untrue, respectively. (How do you compare how long branches live? Branches are nested. They cannot help living at least as long as any of their parts.)

    Sigh, I dont suppose either of those Nature articles have been made available online?

    Of course all are available online. They’re just behind a ridiculously high paywall.

    If you removed all the unnecessary stuff from DNA in some sort of homo superior experiment, would it make a difference? Would replication be faster and less prone to error, or conversely more so? Any macro effects that an organism would notice?

    Cell size would shrink.

    This is what confuses me, because aren’t birds homeothermic? And weren’t some dinosaurs also homeothermic? Yet homeothermy on the chart above is listed only on the mammalian side. So is this convergent evolution or something inherited from the distant ancestor?

    It’s convergent. On the one side, crocodiles, tuatara + lizards & snakes, and turtles — three branches that are more closely related to the birds than to the mammals — are poikilothermic; on the other, there are lizard-shaped animals in the distant ancestry of mammals, too, for which poikilothermy is a safe assumption.

    Oddly enough, the wiki article isn’t too bad: Cladistics.

    It is bad. It introduces cladistics as “a philosophy of classification”, which is wrong and wrong, respectively. I’ll dig up better links tomorrow.

    Didn’t he originally propose that they evolved from Carnivora, and their ungulate affinities have only been worked out recently?

    Yep.

    But what if we happened to find a currently living animal in some remote place, whose common ancestor with modern therians lived some 50-100 million years before that of platypus? Mammal? or reptile? or would we just have to consider it “some percentage”? Whether or not it retains a similarity to that common ancestor, I think by a cladistic view we would have to consider it “partly mammal” in just the same way we would consider the common ancestor.

    Cladistics has nothing to do with this. You are talking about nomenclature. In nomenclature, I’d use definitions for taxon names.

    However the only person I personally know that was killed by a snake

    Casually tosses off that he knows someone who was killed by a snake, as if that were normal… :-)

    …no they’re not. whales are tetrapods (even if they don’t have four feet anymore), and tetrapoda and osteichthyes are sister clades, under gnathostomata.

    No, no, no. If we kindly ignore all fossils, the sister-group of Tetrapoda is Dipnoi, the lungfishes. The sister-group of these two together is Latimeria. All three together form Sarcopterygii (the lobefins). The sister-group of Sarcopterygii is Actinopterygii (the rayfins), and this is what all “normal fish” are. Sarco- and Actinopterygii together form a clade that is, unfortunately, called Osteichthyes by most workers (though some prefer Neoteleostomi, Euteleostomi, or Osteognathostomata). Osteichthyes and Chondrichthyes (the cartilaginous fishes — chimeras and sharks-including-rays) together form Gnathostomata.

  125. #127 David Marjanovi?, OM
    May 13, 2008

    The same tree again:

    Gnathostomata
      |–Chondrichthyes
      `–Osteichthyes
           |–Actinopterygii
           `–Sarcopterygii
             |–Latimeria
             `–+–Dipnoi
               `–Tetrapoda

    (If I included just the most interesting fossils, I'd inflate this tree to 10 times its size.)

  126. #128 David Marjanovi?, OM
    May 13, 2008

    Cosmetic update:

    Gnathostomata
      |–Chondrichthyes
      `–Osteichthyes
           |–Actinopterygii
           `–Sarcopterygii
                |–Latimeria
                `–+–Dipnoi
                   `–Tetrapoda

  127. #129 Ichthyic
    May 13, 2008

    cladistics:

    basic:

    http://evolution.berkeley.edu/evolibrary/article/phylogenetics_05
    http://www.fossilnews.com/1996/cladistics.html

    more detailed, with critique:
    http://www.palaeos.com/Systematics/Cladistics/cladistics.htm

    @David:

    do you spend any time perusing Cladistics?

    Is it a decent journal, in your opinion?

  128. #130 Sven DiMilo
    May 13, 2008

    I am a proud sarcopterygian!
    (I’m sporting internal nares as an optional upgrade)

  129. #131 Owlmirror
    May 14, 2008

    I don’t have much to contribute, but I did just finish The Ancestor’s Tale, and Dawkins’ Platypus’s Tale appears to have been drawn largely from:


    Manger, P. R. & Pettigrew, J. D (1995) “Electroreception and the Feeding Behaviour of Platypus (Ornithorhynchus anatinus: Monotremata: Mammalia)”, Philosophical Transactions of the Royal Society B: Biological Sciences 347: 359—381 (DOI: 10.1098/rstb.1995.0030 )

    It has previously been shown that platypus are sensitive to small electrical fields. It was predicted that platypus use their electrosensitivity to locate the source of foodstuffs on the bottom of the freshwater river systems in which they live, because the platypus are nocturnal, and close their eyes, ears and nostrils while underwater. In this paper we demonstrate for the first time that platypus are indeed sensitive to electrical waveforms that imitate the electromyogenic potential’s of fleeing prey, and following stimulation show interest in area surrounding the electrodes. We also show that platypus respond with a reflex after stimulation with a square wave, and show that this reflex is directionally tuned to the origin of the electrical pulse, with a preferential sensitivity axis 40 times more sensitive than non-preferred axes. The strong directional sensitivity explains previous discrepancies in the lowest threshold for platypus electroreception, which we find to be 50 mV cm-1. Platypus are also sensitive to galvanic fields. We present the data in the light of standardized feeding strategies of the platypus, and discuss the integration of the findings into these feeding strategies. We surrounded our platypus enclosure with a Faraday cage, theraby eliminating excess electrical noise, a suggested new addition to the husbandry regime of platypus.

    Monotremata represent, yo.

  130. #132 arachnophilia
    May 14, 2008

    @David Marjanovi?, (#126-128):

    yes, okay that was an update i must not have been aware of. ironically, i knew that it probably should be that way, with tetrapods under or as a sister group to lungfish due to their ancestry (you know, NOT ignoring those fossils). so, i stand corrected: whales are osteichthyes. :P

  131. #133 Owlmirror
    May 14, 2008

    Another reference from The Ancestor’s Tale, which I hadn’t noticed when I posted before:


    Pettigrew, J. D.; Manger, P. R. & Fine, S. L. B. (1998) “The sensory world of the platypus”, Philosophical Transactions of the Royal Society B: Biological Sciences 353: 1199—1210 (DOI: 10.1098/rstb.1998.0276 )

    Vision, audition and somatic sensation in the platypus are reviewed. Recent work on the eye and retinal ganglion cell layer of the platypus is presented that provides an estimate of visual acuity and suggests that platypus ancestors may have used vision, as well as the bill organ, for underwater predation. The combined electroreceptor and mechanoreceptor array in the bill is considered in detail, with special reference to the elaborate cortical structure, where inputs from these two sensory arrays are integrated in a manner that is astonishingly similar to the stripe-like ocular dominance array in primate visual cortex, that integrates input from the two eyes. A new hypothesis, along with supporting data, is presented for this combined mechanoreceptive-electroreceptive complex in platypus cortex. Bill mechanoreceptors are shown to be capable of detecting mechanical waves travelling through the water from moving prey. These mechanical waves arrive after the electrical activity from the same prey, as a function of distance. Bimodal cortical neurones, sensitive to combined mechanical and electrical stimulation, with a delay, can thus signal directly the absolute distance of the prey. Combined with the directional information provided by signal processing of the thousands of receptors on the bill surface, the stripe-like cortical array enables the platypus to use two different sensory systems in its bill to achieve a complete, three-dimensional ‘fix’ on its underwater prey.

    Unlike the first cite that I posted, the full text of this paper is freely available. It includes the “map” in the platypus brain of its body, showing the huge amount of space allocated to the bill. Dawkins suggests that this be called the platypunculus, after the human homunculus described by Wilder Penfield.

    Searching on Pettigrew and Manger finds more platypus references, including one titled “Electroreception in monotremes”.

  132. #134 Katharine
    May 14, 2008

    Apparently, my reply to Lynnai and Jay got lost in the interweb.

    Lynnai, I apparently misunderstood what you were saying. Thank you for clarifying what you said – so you do know evolution works.

  133. #135 David Marjanovi?, OM
    May 14, 2008

    more detailed, with critique:
    http://www.palaeos.com/Systematics/Cladistics/cladistics.htm

    Some of it based on misunderstandings.

    do you spend any time perusing Cladistics?

    Rather too little.

    Is it a decent journal, in your opinion?

    Mostly, but it does occasionally publish trash. Why are you asking?

    We surrounded our platypus enclosure with a Faraday cage, theraby eliminating excess electrical noise, a suggested new addition to the husbandry regime of platypus.

    Cool :-)

    due to their ancestry (you know, NOT ignoring those fossils).

    By “ignoring the fossils” I only meant “not showing them in the tree”, not “ignoring the phylogenetic information they contain” — though the very same tree usually comes out of analyses of molecular data alone, too.

  134. #136 Sven DiMilo
    May 14, 2008

    the very same tree usually comes out of analyses of molecular data alone

    Speaking of which, David, please stop wasting time on Pharyngula; I am counting on you to figure out where turtles really belong, so hurry up about it! (:

  135. #137 MIkeG
    May 14, 2008

    David Marjanovi?, OM:

    It is bad. It introduces cladistics as “a philosophy of classification”, which is wrong and wrong, respectively. I’ll dig up better links tomorrow.

    Well, crap. I skimmed it and should have paid better attention. Mea culpa. Also, I’m not much of a cladist, so I probably missed plenty of other wrongnesses. I’ll wait for your links and try to grock them in fullness.

    Ichthyic, thanks for the links. I have some reading to do. I can’t think of a better way to spend a nice evening.

  136. #138 MIkeG
    May 14, 2008

    Sven, the turtles are clearly mammals, too. I know they lay eggs, but the ones in our pond are fuzzy with very fine green tinted fur. Maybe grouping with the sloths, with a loss of placentas (ae?) and convergent evolution of yolk-like proteins.

    That or they’re covered with algae.

    I wish there was some guideline about preferring complicated, elaborate hypotheses or ones with fewer assumptions…

  137. #139 MIkeG
    May 14, 2008

    From Ichthyic’s last link:

    In that way phylogenetics is not and cannot be a hard science in the way chemistry, physics, or even neontological (study of extant species) biology is.

    Yikes! I know there are some vagaries involved in phylogeny and cladistics, but that quote ought to stimulate some discussion.

  138. #140 robbrown
    May 15, 2008

    Glad to see I was right about the whales. :) (not that it was central to my point)

    But David, I stand by my statement that if the most recent common ancestor of the therians and a some other living animal is a “partial mammal” (i.e. a proto-mammal that is in the borderline area between non-mammals and mammals), then cladistic-based nomenclature would say that the modern animal is “partial mammal” in the exact same way.

    I think we have to agree that the line between mammal and non-mammal is blurry if looking at our ancestors (right?). Secondly, if a group is monophyletic, that means that every two animals in the group must be “connected” entirely by animals also within the group (right?). Therefore, if the most recent common ancestor of two animals is a proto-mammal (i.e. not fully a mammal), then both animals cannot fully be mammals.

    I don’t suggest this is true of the platypus (its common ancestor with therians was more recent than the protomammals), but theoretically it could be true if such an animal were discovered.

  139. #141 Sven DiMilo
    May 15, 2008

    Taxonomy is about definitions. Definitions are both explicit and arbitrary. If people want to define Reptilia to be identical to the clade also called Sauropsida, fine. But that is not going to change the way other people use and understand the informal term “reptile.” Similarly, a neontologist may define “mammal” as an animal with hair and lactation, whereas a paleontologist will prefer the single-jawbone definition. There were certainly synapsids that were not mammals by either definition. You can call such animals “non-mammalian synapsids” or “mammal-like reptiles,” but as long as everybody knows which animals are referenced (and I would suggest that there is little or no ambiguity in either term), who cares? Go ahead and define formal taxonomic levels explicitly and rigorously and more power to ya, I’m glad some people are interested in doing so. But it’s unrealistic and kind of elitist and/or arrogant to suggest that we then need to scrub the informal English language to conform to formal taxonomic rigor.
    For myself, I intend to keep using paraphyletic terms like reptile, monkey, fish, lizard, dinosaur, prokaryote, and algae in my everyday, informal conversation–even though as a biologist I “know better” in a formal sense–because everybody knows what they mean. *shrug*

  140. #142 David Marjanovi?, OM
    May 15, 2008

    Yikes! I know there are some vagaries involved in phylogeny and cladistics, but that quote ought to stimulate some discussion.

    Well, it’s hard to disprove anything in phylogenetics; it relies mostly on the other part of the scientific method, Ockham’s Razor.

    then cladistic-based nomenclature would say that the modern animal is “partial mammal” in the exact same way.

    There is no such thing as cladistic-based nomenclature. What did you mean?

    Taxonomy is about definitions.

    Nomenclature is.

    Similarly, a neontologist may define “mammal” as an animal with hair and lactation, whereas a paleontologist will prefer the single-jawbone definition.

    AFAIK all of the paleontologists in that field now use one of two phylogenetic definitions: either “the most recent common ancestor of [token monotreme], [token marsupial] and [token placental], and all its descendants”, or “the most recent common ancestor of [type species of Sinoconodon] and [token monotreme, marsupial, and/or placental]“.

    And when you use phylogenetic definitions, there is nothing blurry about the beginnings of taxa. Once upon a time there was a non-mammalian mammalimorph that laid an egg out of which a mammalian mammalimorph hatched. “The most recent common ancestor” is a single individual for asexual organisms, and a breeding pair or otherwise small part of a population for sexual organisms… in which case blurriness might admittedly exist between cytogamy (fusion of gametes) and karyogamy (fusion of their nuclei) :o)

  141. #143 David Marjanovi?, OM
    May 15, 2008

    Speaking of which, David, please stop wasting time on Pharyngula; I am counting on you to figure out where turtles really belong, so hurry up about it! (:

    One side project after the other, please. Right now I have an analysis of amphibian phylogeny running on this computer.

  142. #144 David Marjanovi?, OM
    May 15, 2008

    In the words of Tom Holtz: “REALLY good introduction to cladistics!!

    Enjoy.

  143. #145 Ichthyic
    May 15, 2008

    Mostly, but it does occasionally publish trash. Why are you asking?

    for exactly that: an indication of just how much trash it lets by.

    I’ve only glanced at articles from it directly relating to other work I have done in the past (I once was working on a reclassification of the Pomacentridae).

  144. #146 Ichthyic
    May 15, 2008

    Yikes! I know there are some vagaries involved in phylogeny and cladistics, but that quote ought to stimulate some discussion.

    just to be clear, I thought it good to post some more “argumentative” positions, but I don’t agree with the implied conclusion of that last link. it sounds way too much like the old: “Biology is not a hard science arguments”

    the methods are sound, even if there is argument over some of the details.

    Damn, but I got so tired of the endless debates over phylogenetics between the old school zoologists and the molecular biologists when i was a grad student at Berkeley.

  145. #147 David Marjanovi?, OM
    May 16, 2008

    From what little I can tell, the trash in Cladistics is mostly in the more opinionated pieces.

  146. #148 Philip Bruce Heywood
    May 16, 2008

    I’ll wager none of them asked you to describe the actual train of events whereby HOMO SAPIENS (Linnaen terminology! shock, horror!) ceased interbreeding with its great, great, ….. grandfather’s species. So I’ll ask you now, on behalf of people everywhere,who haven’t been in the bush too long, to do so. Avoid religious verbiage.

    Follow this with the non-mystical account of how genetically distinct (Linnaen) fish species A got to be involved in the linneage of genetically distinct fish species B, in the same ocean. Defer to the facts, as supplied by geology. It happened. The fossils don’t lie. Neither did Linnaeus – although he certainly didn’t know everything.

    Why is it so quiet around here?

    Biology/palaeontology aren’t quite the same as physics and chemistry, but there is technical certainty there of a deep and profound type. For living organisms to be created and to survive, information systems of a different, higher order are required. Enter the new developments, especially quantum style information technology. And don’t worry, they will show that Linnaeus wasn’t quite off the rails, the geologic record means what it says, and microbiology in the light of said specialist information technology, agrees with both them and the man in the street, provided he hasn’t been in the bush, or at Berkeley, too long.

    Is that a pin, dropping?

  147. #149 Philip Bruce Heywood
    May 16, 2008

    My above post was directed to Ichythic.

  148. #150 Sven DiMilo
    May 16, 2008

    I ackowledge the conceptual purity and unambiguous non-blurriness of phylogenetic definitions, but a paleontologist who digs up a fossil skull and asks the first question “what is it?” does not start thinking about common ancestors, she counts jawbones. You can apply phylogenetic definitions once you have sufficient characters and specimins to run your matrix etc.; that’s what systematists do and more power to ‘em (amphibians? come on, who cares! do the damn turtles already!), but a taxonomist has to use character-based definitions in practice. (Yes, I’m aware of the difference between a diagnosis and a definition).
    But that’s not what we were arguing about above.

    My above post was directed to Ichythic.

    …and I know he appreciates it!

  149. #151 Philip Bruce Heywood
    May 17, 2008

    Perhaps he’d appreciate Shakespeare as well: how about;

    Rosalind. ‘Tis he: slink by, and note him.
    Jaques. I thank you for your company; but, good faith, I had as lief been myself alone.
    Orlando. And so had I; but yet, for fashion sake, I thank you too for your society.
    Jaques. God buy you; let’s meet as little as we can.
    Orlando. I do desire we may be better strangers.
    Jaques. I pray you mar no more trees with writing love songs in their barks.
    Orlando. I pray you mar no more of my verses with reading them ill-favouredly ……. .

    Shakespeare was a cool dude, eh?

  150. #152 disinterested observer
    May 18, 2008

    Just to go off on a tangent …

    Australians are cautious about snakes, but most Australians realise that you don’t really have much to worry about. There appear to have been about 40 snake related deaths in Australia over the last 27 years, which roughly approximates to an annual risk of less than one in 13 million.

    http://members.iinet.net.au/~bush/wadeaths.html

    Whereas in India there are now about 50,000 snake related deaths a year (and India does not have a population 50,000 times that of Australia)

    http://members.iinet.net.au/~bush/wadeaths.html

  151. #153 disinterested observer
    May 18, 2008
  152. #154 Owlmirror
    May 18, 2008

    And when you use phylogenetic definitions, there is nothing blurry about the beginnings of taxa. Once upon a time there was a non-mammalian mammalimorph that laid an egg out of which a mammalian mammalimorph hatched. “The most recent common ancestor” is a single individual for asexual organisms, and a breeding pair or otherwise small part of a population for sexual organisms

    Maybe I’m just not understanding something here…

    Wouldn’t all of the mammalian mammalimorph’s breeding partners be non-mammalian mammalimorphs? And would it not therefore be some time before all of the traits that definitely are those of mammalian mammalimorphs are even a significant fraction of the mammalimorph population, and even longer before the non-mammalian and mammalian populations diverged completely?

    And if the most recent common ancestor is “a breeding pair or otherwise small part of a population”, then why are mitocondral Eva and Y-Adam thousands of miles apart and separated by many thousands of years?

    There’s a part of The Ancestor’s Tale where Dawkins rants about the “discontinuous mind”; the very idea of thinking that things are all one way or another. He specifically offers this as part of the Salamander’s Tale; which is about the ring species of salamander of the genus Ensatina around California’s Central Valley.

    I think his point in his rant is that while traits are discontinuous, combinations of traits are not always so easy to classify. He also mentions taxonomic “lumpers” (prefer to classify into a few large groups) and “splitters” prefer to classify into a lots of small groups).

    If I understood correctly, I think he is simply saying that taxonomy is not always a simply binary sort of thing. Clarification would be welcome…

  153. #155 Philip Bruce Heywood
    May 19, 2008

    I’m not sure I’m any use to you, Mr. Mirror. I have enough trouble, trying to get applicable Shakespeare stuff, leave alone this zoology. Don’t know how you people do it. If it’s any enlightenment, my palaeontology lecturer, who was no slouch, discussed at length the Species Problem, and concurrently he made clear that classification of fossil species ideally is bound up in the concept of reproductively discreet units. Now I suppose, given time, in the wild – which palaeontology sees the results of – organisms do leave remains that are highly suggestive of, and often are clear proof of – said reproductively definable units. The zoo-o-wizzard, on the other hand, gets (in geologic time) a frozen snap shot: and going on these Californian Salamanders, and other organisms, classification of populations in a snap shot needn’t be taxonomically cut and dried. One wonders, if they were to be preserved over millions of years, what these salamanders would come out as. Would time recombine them as clearly one species, or are they in the process of getting ready to split?

    Yourself being a wise man, Mr. Owl, might consider, in addressing these conundrums: 1) There are no common ancestors, in the ‘blood descent’ meaning. Life was passed on, species to species; at transformation, information technology re-programmed necessary parts of the DNA (presumably somehow incorporating new information fed back from the living conditions): the immune system, species lock, and what have you, were tripped, new species were brought into the world as genetically discreet units through information technology. Look to humanly engineered cloning, but do it through (quantum level) information technology, and re-program the clone as a new species. That’s possible: common descent evolution is impossible.
    2) It seems likely under this scenario that species might show symptoms of ‘fusing’ together – perhaps species that readily hybridize with each other were very close, time-wise and genetics-wise, and some weirdo stuff, happening in the wild, mught be a relection of this.
    3) The role of environment in speciation is as a source of information (presumably recorded somehow in the organism), and presumably also as a trigger, perhaps to set the re-programming rolling, certainly to trigger new expressions of latent genetic information. It follows that isolation, leading to the experiencing of novel environmental circumstances by some species members, could be a factor in speciation. Thus, ring-species might be indicative that something was afoot, evolution-wise; or the ring might fade back into an homogenous population once again, depending on circumstances.

    Reflecting on this, Mr. Mirror, we deduce that Nature has a few oddities up its sleeve. One thing we may hang our hats on: although an upcoming speciation event amongst those salamanders or such like organisms might or might not be indicated by their current configuration, they are not in the process of speciating. That’s a quantifiable, dramatic event, which is not being observed in our biosphere because we no longer have access to what the Bible calls the Tree of Life (information technology communications system capable of DNA ETC. re-programming). Dramatic morphing amongst microbes ETC, detrimental to life, yes; speciation amongst higher organisms, no.
    Taking these things into consideration, as a complete non-expert, I would say, think long-term, endeavour to comply with Linnaen, objective, nomenclature, factor in all the different things that can happen to a species, wisely reflect thereon, as you always do.
    Well, I don’t know: “This goes deep; yet we shall fathom it” – that’s Shakespeare, isn’t it?

  154. #156 David Marjanovi?, OM
    May 19, 2008

    I ackowledge the conceptual purity and unambiguous non-blurriness of phylogenetic definitions, but a paleontologist who digs up a fossil skull and asks the first question “what is it?” does not start thinking about common ancestors, she counts jawbones. You can apply phylogenetic definitions once you have sufficient characters and specimins to run your matrix etc.; that’s what systematists do and more power to ‘em (amphibians? come on, who cares! do the damn turtles already!), but a taxonomist has to use character-based definitions in practice. (Yes, I’m aware of the difference between a diagnosis and a definition).

    Apparently not, no.

    Firstly, we need both definitions and diagnoses. Diagnoses are not fixed under any system of nomenclature; they depend on the phylogenetic hypothesis (unless you want to allow polyphyletic taxa). So, look at the characters, do a phylogenetic analysis with them, optimize the characters on the tree to see which changes diagnose which clade on this tree, and apply the definitions to see what to call each clade.

    Secondly, there’s a type of definition called apomorphy-based. It takes the form “the first organism to possess feature X as inherited by organism Y, and all its descendants”. In other words, you can have characters in definitions. It’s tricky — the character(s) must be described very precisely to avoid problems with intermediate states, and when the body part in question is unknown, we can end up with not being able to tell if the organism in question is part of the taxon in question or not, even if its phylogenetic position is completely resolved –, but it’s possible.

    Thirdly, phylogenetic nomenclature makes taxonomy (in most meanings of that word) useless. There’s phylogenetics, and there’s nomenclature. That’s enough.

    Wouldn’t all of the mammalian mammalimorph’s breeding partners be non-mammalian mammalimorphs?

    By definition, not those that are our ancestors. All others, yes.

    And would it not therefore be some time before all of the traits that definitely are those of mammalian mammalimorphs are even a significant fraction of the mammalimorph population, and even longer before the non-mammalian and mammalian populations diverged completely?

    Of course. But Mammalia is not defined by a combination of traits!

    And if the most recent common ancestor is “a breeding pair or otherwise small part of a population”, then why are mitocondral Eva and Y-Adam thousands of miles apart and separated by many thousands of years?

    These are the MRCAs of our mitochondria and our Y chromosomes, respectively, not the MRCAs of the whole of us. I’m talking cell trees, not gene trees.

    There’s a part of The Ancestor’s Tale where Dawkins rants about the “discontinuous mind”; the very idea of thinking that things are all one way or another.

    For species, he’s right on, because most species concepts don’t correspond to clades. If we use, say, interbreeding as a criterion, then species are very blurry affairs indeed. (Obligatory reminder: there are at least 25 species concepts out there, and no consensus; and, depending on the species concept, there are between 101 and 249 endemic bird species in Mexico.)

    For phylogenetic nomenclature, it’s a bit different. All organisms indeed are either one thing or not — but they never stop being another. Traditionally, if you’re a mammal, you’re not a reptile. In phylogenetic nomenclature, if you’re a mammal, you’re still an amniote, and your descendants will never stop being amniotes.

    —————————

    I’ll wager none of them asked you to describe the actual train of events whereby HOMO SAPIENS (Linnaen terminology! shock, horror!) ceased interbreeding with its great, great, ….. grandfather’s species. So I’ll ask you now, on behalf of people everywhere,who haven’t been in the bush too long, to do so.

    First, where’s the horror? I don’t understand.

    Second, you got the terminology wrong. It’s not “HOMO SAPIENS”, it’s Homo sapiens, mind the capitalization and the italics.

    Third, you seem to have a very weird idea of the fossil record. Can you bring us the bones of any of your great10-grandfathers? No? Then why do you expect us to bring you the bones of all of your great3,000,000-grandfathers, let alone a complete record of their romantic encounters and complete sequences of their genomes?

    genetically distinct (Linnaen) fish species

    You act as if Linnaeus had had a species concept other than “I know it when I see it”. This is, you see, not the case. Never mind the fact that neither the word “gene” nor the concept had yet been invented.

    What do you even mean by “genetically distinct”? Surely you don’t mean “not identical twins”? Because that’s all it means when you don’t add any further explanations.

    For living organisms to be created and to survive, information systems of a different, higher order are required.

    Please explain what you mean, instead of hiding behind poetic fog.

    Enter the new developments, especially quantum style information technology.

    This shows you don’t understand what “quantum” means.

    the man in the street

    Only Americans and Third-World people are creationists anymore. Don’t tell me you didn’t know that.

    Next you’ll probably tell us you have any idea of geology…

    Would time recombine them as clearly one species, or are they in the process of getting ready to split?

    This depends on the environment. Increase the gene flow (perhaps by making the area around the Death Valley better country for salamanders to live in), and they will merge back. Decrease the gene flow, and keep it that way for long enough, and they will lose the ability to merge, even if it takes twenty million years.

    There are no common ancestors, in the ‘blood descent’ meaning.

    This is not a conundrum. This is a claim. An extraordinary claim that, by being an extraordinary claim, requires extraordinary evidence.

    This evidence, my friend, you will put up, or you will shut up. That’s how science works. Men are from Mars, women are from Venus, scientists are from Missouri. Show us.

    presumably somehow incorporating new information fed back from the living conditions

    Ah, a Lamarckist. You have been sleeping for the last 60 years. Why are Jews still born with foreskins?

    the immune system, species lock, and what have you, were tripped

    Huh? What do you mean by “species lock”? And what does the immune system have to do with species?

    Look to humanly engineered cloning, but do it through (quantum level) information technology, and re-program the clone as a new species. That’s possible: common descent evolution is impossible.

    This is treknobabble.

    Has it never diffused through your osteosclerotic parietals that using technical terms at random will give people the impression that you don’t understand what you are talking about?

    It seems likely under this scenario that species might show symptoms of ‘fusing’ together – perhaps species that readily hybridize with each other were very close, time-wise and genetics-wise, and some weirdo stuff, happening in the wild, mught be a relection of this.

    If you were wrong, how would you know?

    It’s easy: ejaculate into an orang-utan and look what happens. Nothing happens. (I’m told some people have tried, and not even for scientific purposes, but for personal fun.) When species can interbreed, they can fuse (though in that case they were, under the two “Biological Species Concepts”, still the same species to begin with!). When they can’t interbreed anymore, they can’t fuse. Easy, no?

    The role of environment in speciation is as a source of information (presumably recorded somehow in the organism)

    Lamarckism again!

    No, dude, no. There is no way how information from the environment could be recorded in an organism, and there is no evidence that it ever happened — to the contrary, see above.

    It follows that isolation, leading to the experiencing of novel environmental circumstances by some species members, could be a factor in speciation. Thus, ring-species might be indicative that something was afoot, evolution-wise; or the ring might fade back into an homogenous population once again, depending on circumstances.

    This is entirely correct, but you should have explained the role of selection in it: “the experiencing of novel environmental circumstances by some species members” causes those members to have different success in reproduction than they would have had otherwise. Those members who, because of their slightly different genome, can have more offspring in the new environment have more offspring there. And that’s evolution by mutation and natural selection.

    they are not in the process of speciating. That’s a quantifiable, dramatic event

    Wrong.

    Dramatic morphing amongst microbes ETC, detrimental to life, yes; speciation amongst higher organisms, no.

    Define “higher”, please — but I’m not holding my breath. I’ll just mention Culex molestans, the London Underground mosquito.

    Linnaen, objective, nomenclature

    :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D

    Nobody has pretended in the last 300 years that it’s objective. It isn’t. Subjectivity is inbuilt in it in several crucial places.

    wisely reflect thereon

    No, no, no, no, no. Not Aristotle. Francis Bacon.

    Observe, and read up on what others have observed. Thinking is necessary, but thinking alone will get us nowhere. Did get us nowhere — we tried, for centuries.

    as a complete non-expert

    You don’t need to tell us. It’s screamingly obvious already. What you need to tell, to yourself, is that you should stop assuming that we don’t know more about this field than you do either. Ignorance is fine. Assuming that everyone is just as ignorant as oneself is a recipe for delusion.

    (BTW, as far as I know, Owlmirror is a she.)

  155. #157 David Marjanovi?, OM
    May 19, 2008

    Silly me. I filled almost 9 laptop screens and still forgot to mention all those plants that hybridized and created polyploid hybrid species right in front of our eyes. Or are plants not “higher organisms” by your ineffable criteria?

    There’s a nice list of observed speciations somewhere on http://www.talkorigins.org. Look it up. Keep in mind that, while not all of the happenings described there are speciations under every species concept, all of them are speciations under several species concepts.

  156. #158 Owlmirror
    May 19, 2008

    Sorry, I’m still trying to wrap my brain around this…

    But Mammalia is not defined by a combination of traits!

    I’m trying to reconcile this with what you responded to Sven DeMilo, in explaining apomorphy… What is the difference between a “character” and a “trait”, such that “In other words, you can have characters in definitions.”?

  157. #159 Philip Bruce Heywood
    May 19, 2008

    Don’t bother trying to reconcile it, OM. (Owlmirror). Mr Marjonovic is an OM, himself. I think that stands for something that means he fills up cyberspace on PHARYNGULA, writing stuff withOut Meaning. ‘Bout all I picked up was that he stutters – d-d-d-d-d-ecidedly so. AH, the London underground mosquito. Something like the fruit fly, I take it. Shakespeare got bitten by them. They infest theatre cellars. He swatted so many, they mutated into lacewings. This brave new world, that hath such creatures in it.

  158. #160 Ichthyic
    May 19, 2008

    Phillip, do shut up.

  159. #161 Steve_C
    May 19, 2008

    OM = Order of the Molly

    Given to those who have earned the accolades of fellow commenters.

    PBH won’t be getting one.

  160. #162 Ichthyic
    May 19, 2008

    I think Phillip is bucking for the OTHER award:

    http://scienceblogs.com/pharyngula/plonk.php

    I wonder what color curtains he likes?

  161. #163 MIkeG
    May 19, 2008

    Ichthyic:

    just to be clear, I thought it good to post some more “argumentative” positions, but I don’t agree with the implied conclusion of that last link. it sounds way too much like the old: “Biology is not a hard science arguments”

    I tend to agree. What really is a hard science? Just the stuff with fewer variables, IMHO. Stellar astrophysicists don’t have to deal with interacting molecules, chemistry and sex (etc.). Biology is harder, if you ask me.

    I didn’t mean to bring up the old discussion about the “hardness” of biology, relatedness and how to figure it out. That quote triggered my “Oh, yeah? Let’s fight!” and my “Well, DUH” circuits at the same time. I’s a little weird learning the cladistics by parsimony using apomorphies, etc., in undergrad and going into exclusively molecular work later. (Bacteria don’t have too many easily useable traits, unless you have the genome.)

    OK, never mind all that, Let’s make fun of Philip!
    Mutated into Lacewings?
    There’s nothing for it but to laugh.

  162. #164 MIkeG
    May 19, 2008

    By “Biology is harder”, I mean harder to get a grip on. I switched uses of the word harder, there. Sorry.

  163. #165 Ichthyic
    May 19, 2008

    What really is a hard science? Just the stuff with fewer variables, IMHO.

    That’s about as quick and accurate a summation as I’ve seen.

    Biology is harder, if you ask me.

    me too.

    It’s far easier IMO to plan and execute a chemistry experiment in a lab, than a test of a behavioral hypothesis in the field (having done both many times).

    …and it’s often not even the many known variables that are difficult enough to control for in the field; it’s the UNKNOWN ones that kick ones proverbial ass.

    ask a chemist or a physicist if they ever had problems executing an experiment because five hurricanes sequentially marched through their lab.
    ;)

  164. #166 Ichthyic
    May 19, 2008

    By “Biology is harder”, I mean harder to get a grip on.

    it works both ways, actually.

  165. #167 spurge
    May 19, 2008

    Biology is a pain even when you are using well characterized bugs in the lab.

    The little bastards have their own agenda and can destroy the most well planned experiment.

  166. #168 Owlmirror
    May 19, 2008

    CLOWN 1: Who be this babbler, this gibbering child of nature, this addle-pated mooncalf?

    CLOWN 2: Doth he not scribe his name right well?

    CLOWN 1: The first part hints that he loveth the horse.

    CLOWN 2: Aye, perhaps too well. Mayhap a horse kicked him in the head before fleeing like the wind.

    CLOWN 1: ‘Twould explain much.

    CLOWN 2: And the second part?

    CLOWN 1: ‘Tis a name from the cold north.

    CLOWN 2: Where the men, ’tis said, are very manly.

    CLOWN 1: And the very sheep, ’tis said, live in fear.

    CLOWN 2: And the third part?

    CLOWN 1: Mayhap ’tis a riddle.

    CLOWN 2: Be he a tree?

    CLOWN 1: Or hath he a stiffness of his focative root?

    CLOWN 2: Perhaps he tells of his head.

    CLOWN 1: If so, he tells all that he hath termites, or dry rot.

    CLOWN 2: And if ’tis his root, he shall find no satisfaction, for all he come near shall fear splinters.

    CLOWN 1: Wherefore horse and sheep flee him!

    CLOWN 2: Thou hath unriddled him, forsooth!

  167. #169 Ichthyic
    May 19, 2008

    The little bastards have their own agenda and can destroy the most well planned experiment.

    heh.

    I had a buddy in grad school who tried to do his thesis on scorpion behavior who would most adamantly agree with you.

    OTOH, we did have a lot of fun betting on the outcomes of some of his experiments.
    :P

  168. #170 MIkeG
    May 19, 2008

    Spurge, isn’t that called the Harvard conjecture?

    “In the best controlled experiment, the animals will do whatever the hell they feel like.” Paraphrased.

  169. #171 spurge
    May 19, 2008

    scorpions? Way too dangerous for my taste.

    E.Coli and Yeast are more my speed.

    If they get out of line a little bleach will set them straight.

  170. #172 windy
    May 19, 2008

    #168: Most excellent accomplished lady, the heavens rain odours on you!

  171. #173 Ichthyic
    May 19, 2008

    If they get out of line a little bleach will set them straight.

    genocidal maniac! It’s no wonder Stein associates science with Naziism!
    ;)

  172. #174 spurge
    May 19, 2008

    MikeG

    That quote is very familiar but I don’t remember where I heard it.

    My google skills failed to find anything.

  173. #175 spurge
    May 19, 2008

    Tis true.

    I have killed millions for science.

    Who knew that a “mini prep” was a WMD?

  174. #176 MIkeG
    May 19, 2008

    spurge, I can’t remember where I heard it either.

    I’m with you, though. I have the autoclave ready and waiting. Oddly enough, there are no protesters at my door…

    Wait, is a pressurized steam chamber the same as a gas chamber? OMG! I’m a microbe killing NAZI !!!!1!!!1!11

  175. #177 MIkeG
    May 19, 2008

    Apparently, “I just wanted the plasmids” isn’t a valid defense…

  176. #178 spurge
    May 19, 2008

    “I just wanted the plasmids”

    We can call that the biotech defense.

  177. #179 Ichthyic
    May 19, 2008

    OMG! I’m a microbe killing NAZI !!!!1!!!1!11

    expect the animal rights groups to be picketing your lab next week!

    I’m only half kidding about that, btw. Ah, the stories I could tell you about the animal rights groups at Berkeley…

  178. #180 Ichthyic
    May 19, 2008

    We can call that the biotech defense.

    “If the pipette doesn’t fit, you must acquit!”

  179. #181 Owlmirror
    May 19, 2008

    “Under the most rigorously controlled conditions of pressure, temperature, volume, humidity, and other variables the organism will do as it damn well pleases.”

  180. #182 Philip Bruce Heywood
    May 19, 2008

    Why shouldn’t they picket your lab? Your great great grandfather was a microbe, don’t forget.

  181. #183 Ichthyic
    May 19, 2008

    not the orginal cite, but that one is listed as one of “Murphy’s laws”:

    http://www.murphys-laws.com/murphy/murphy-technology.html

  182. #184 Ichthyic
    May 19, 2008

    Phillip, do shut up.

  183. #185 spurge
    May 19, 2008

    It was not my fault!

    I was just following the protocol!

  184. #186 Owlmirror
    May 19, 2008

    The phrase that I am pretty sure is the common one (the UCA?) for the phrase is “damn well pleases”. Searching on that and “Harvard Law” and “(animal|organism)” yields more than a few variants:

    “Under controlled conditions of light, temperature, humidity, and nutrition, the organism will do as it damn well pleases.”

    and

    “Under precisely controlled experimental conditions, the test animal does as it damn well pleases.”

    and

    “Under the most rigorously controlled experimental conditions that can be devised by the human experimenter, the animal will do just as he damn well pleases”

    The Harvard Law is sometimes called “of Behavior” or “of Behaviorism” or “of Animal Behaviour”.

    Hm. Changing the search from regular google to scholar.google yields 21 hits; the earliest one with text is “Rhetoric in an Age of Science and Technology” by TM Sawyer (1972).

    Although I suspect it to be a bit older. Who can say?

  185. #187 windy
    May 20, 2008

    “If the pipette doesn’t fit, you must acquit!”

    Fit where?

  186. #188 spurge
    May 20, 2008

    “Fit where?”

    Do you really want to know?

  187. #189 windy
    May 20, 2008

    Are we talking regular or multichannel? If it’s the latter, I definitely don’t.

  188. #190 spurge
    May 20, 2008

    We might be talking old school mouth pipetting.

  189. #191 windy
    May 20, 2008

    Yikes!

  190. #192 David Marjanovi?, OM
    May 20, 2008

    What is the difference between a “character” and a “trait”, such that “In other words, you can have characters in definitions.”?

    There is none.

    I should probably have explained what definitions with characters in them (apomorphy-based definitions) look like. For example, suppose Tetrapoda were defined as “the first organism to lack fin rays and have digits homologous with mine, and all descendants of that organism”. In that case, snakes are tetrapods because they are descendants of said beast, even though they have no trace of fingers or toes. The characters in such definitions merely serve to pinpoint the first member of the clade they apply to.

    ———————

    Mr Heywood, if you can’t spell my name, copy & paste it like everyone else. “OM” means this here.

    all I picked up was that he stutters – d-d-d-d-d-ecidedly so.

    You know what a smiley is, don’t you? I laughed for a minute and wrote that down.

    ——————-

    I’s a little weird learning the cladistics by parsimony using apomorphies, etc., in undergrad and going into exclusively molecular work later.

    Why? You simply switched from using morphological apomorphies to using molecular apomorphies. Or (pet-peeve alert) did you use the phenetic method called neighbor-joining?

    —————-

    [...]
    CLOWN 2: Thou hath unriddled him, forsooth!

    Wow. Impressive. Remember “thou hast” and get yet another Molly nomination.

    —————-

    Who knew that a “mini prep” was a WMD?

    Never mind the maxiprep… <shudder>

  191. #193 David Marjanovi?, OM
    May 20, 2008

    Actually, it’s easier if you drop all mention of fin rays from my example definition. It doesn’t even make sense unless I qualify it by “on the extremities” — the tail fin lasted longer (Acanthostega has a very nice one, Ichthyostega had an apparently smaller one of poorly known extent, and in many others the rear half of the tail is unknown) –, and for this example it’s unnecessary.

  192. #194 Philip Bruce Heywood
    May 20, 2008

    David Marjanovic’ : I think I have spelled your name correctly, this time, but you have the better of me with that acute or whatever it is. The best I can do is an apostrophe.
    You mean, Lady Owlmirror? Mademoiselle? Madame! Ms, Mrs, Miss? [Whisks off cloak, lays it over unsavory part of footpath with a flourish, spanks uncouth villein with flat of sword, executes a low bow, retires gracefully. "Ahem. Pardon, Mademoiselle, pardon. My oversight".]

    I hope you’re correct, Marjanovic’. If she turns out to be a – a – a (what’s a male owl? – not a cock, please), I’m in trouble.

    Since we are talking Platypii, the latest news is, they have activated a gene from the extinct Tasmanian Tiger (marsupial dog), by placing it in a mouse. It is at least theoretically possible to revive species in this way.

    Revival of an extinct species is but one fraction of what happened at speciation, but it is an action that implicates at least a fraction of the reality of a full speciation event. I.e., technology is getting to glimpse a pinpoint of light at the end of the speciation tunnel. I am not referring to the ersatz ‘speciation’, achieved by jargon, to which you have referred above. Anyone can prove anything, courtesy of redefining terms. Add some time, some verbiage, and it all happens, in the sweet bye-and-bye.

    Think a while. We are getting to see that pinprick of light at the end of the speciation tunnel. A clear hint as to what happened on those momentous occasions, when, as systematic geology and biology demand, Tasmanian Tigers suddenly appeared where before there was something similar but empirically different. Something that couldn’t successfully breed with T.tigers, even though it bore superficial resemblance to them. The conduit through which life -not genetic integrity – was passed to them.

    We have, as I say, this glimpse. A glimpse of practical reality, regarding speciation. Prof. Archer, now here in Aus., thinks revival is possible, if distant. He is theoretically correct, if the fossils and the biosphere don’t lie. So what mechanism will he be pursuing? The one named Common Descent, by artificially speeding up what you say must have happened in nature? Or the one named Signalled Evolution, which calls in genetic engineering? He, perforce, will be employing rather crude methods. But it is now known to be theoretically possible to achieve such engineering “hands off” – through sophisticated I.T.. Way beyond us right now, but possible.

    Lamarck, Cuvier, Owen, Darwin – they all had something of use. Modern technology shows how. I have attempted to outline said developments, at my site. I invite you to update evolutionary theory. You are, OM, prolific.

    I think OM has something to do with Hindu mantras. Say it often. Totally irrelevant to the topic, although, if repeated enough times, reminiscent, perhaps, of the proposed mechanisms of Common Descent Evolution? Try thinking.

  193. #195 MIkeG
    May 25, 2008

    DavidMarjanovi?, OM

    Why? You simply switched from using morphological apomorphies to using molecular apomorphies. Or (pet-peeve alert) did you use the phenetic method called neighbor-joining?

    Uh-oh I hit a peeve. We use NJ for quick estimates, and usually use maximum likelihood for the final. It’s generally about processor time, and I like having an estimate of divergence that parsimony won’t give you. I admit I’m a bit cavalier with characters in the molecular data, as far as primitive vs. derived, but how else can you deal with it? It’s kind of like throwing everything against the wall and seeing what sticks.

    If you could point me to more information, I’d be grateful. Maybe a good text? All I’ve really studied about it was 1 class for the MS. Hey, I’ve got a ball peen hammer, what other hammer could I possibly need? ;-)

  194. #196 Kevin Wirth
    May 29, 2008

    PZ – you said “We can say with equal justification that we are part reptile, too.”

    Really? I’d like to know which part. Do you have some incredibly compelling evidence for this, or is it just based on more of your evolutionary assumptions?

    Please tell us what the evidence you have for this, because I’m just dying to know. And please, don’t tell us we all descended from reptiles and that’s all you need to say. I’d like to know what markers exist in humans today that would substantiate such a claim.

    And yes, I’m seriously wanting to know.

    Many thanks,

    Kevin

  195. #197 Ichthyic
    May 29, 2008

    Really? I’d like to know which part.

    you’re WAY late to that party, and with nothing to contribute.

    take off your party hat and go home.

  196. #198 Owlmirror
    June 5, 2008

    I’d like to know what markers exist in humans today that would substantiate such a claim.

    Well, all humans, indeed, all mammals, are synapsids. Thus:

    In most vertebrates, the powerful muscles that close the jaw attach to the top of the skull and must pass through a space in the bones of the skull to reach the jaw. Synapsids have one such space; diapsids have two. You can feel how your own chewing muscles pass through a space in your skull (the temporal opening) by placing your hand against the side of your face and biting down. The chewing muscles pass underneath a bony bridge (the zygomatic arch), which is found in all mammals and in their extinct relatives in the Synapsida.

    http://www.ucmp.berkeley.edu/synapsids/synapsidamm.html

    Of course, the synapsids evolved from amphibia, which evolved from lobe-finned fish. You can read about which “markers exist in humans today” of that ancestry, here:

    http://magazine.uchicago.edu/0812/features/fish_out_of_water.shtml

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