…and this is a 
The platypus genome
Category: Evolution • Genetics • Science
Posted on: May 10, 2008 12:32 PM, by PZ Myers
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.
(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.
(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.
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.
Life Science
Comments
Here's a great article on it:
Posted by: Mustafa Mond, FCD | May 10, 2008 12:41 PM
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.
Posted by: Don | May 10, 2008 12:45 PM
Thanks for this. The news commentary was bugging me, too.
And wow, that's a hell of an author list.
Posted by: MIkeG | May 10, 2008 12:49 PM
"Genome analysis"? Wizardry!
Posted by: Rusty | May 10, 2008 12:49 PM
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.
Posted by: PZ Myers | May 10, 2008 12:49 PM
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.
Posted by: PatrickHenry | May 10, 2008 12:51 PM
Yay, cladistics!
Posted by: Karen | May 10, 2008 12:56 PM
This is a great post! Be sure to include this topic in your book.
Posted by: Bill Anderson | May 10, 2008 1:02 PM
I've been hoping all week that you would write on this, thanks very much!
Posted by: Milo Johnson | May 10, 2008 1:04 PM
All extant life forms are transitional, unless they become extinct. Transitional to what is the question?
Posted by: MikeK | May 10, 2008 1:05 PM
Other links:
What the platypus genome is and isn't (Adaptive Complexity)
Platypus sex chromosomes and basal-equals-primitive (Genomicron)
Who are you calling 'primitive'? (Nimravid)
Bad quotes about evolution and genomics (Genomicron)
Posted by: TR Gregory | May 10, 2008 1:06 PM
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.
Posted by: Ted D | May 10, 2008 1:13 PM
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.
Posted by: Richard Harris | May 10, 2008 1:19 PM
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.
Posted by: Bob O'H | May 10, 2008 1:19 PM
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?
Posted by: Longtime Lurker | May 10, 2008 1:28 PM
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!
Posted by: Monado, FCD | May 10, 2008 1:30 PM
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
Posted by: Burt Humburg | May 10, 2008 1:35 PM
I am reminded of the tale of three blind men and an elephant. lol
Posted by: Kagehi | May 10, 2008 1:39 PM
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.
Posted by: Alex | May 10, 2008 1:39 PM
Ah, how I miss these kinds of posts! More, please! :)
Posted by: Dave Carlson | May 10, 2008 1:41 PM
Placental the sister of her brother Marsupial
Their cousin called Monotreme, dead uncle Allotheria
Posted by: Rey Fox | May 10, 2008 1:44 PM
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:
(snip)
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.
Posted by: Mike Haubrich, FCD | May 10, 2008 1:47 PM
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.
Posted by: Peter Ashby | May 10, 2008 1:51 PM
What's with naming dozens of authors on the paper?
Posted by: FishyFred | May 10, 2008 1:51 PM
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.
Posted by: Matt | May 10, 2008 1:52 PM
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....
Posted by: razib | May 10, 2008 2:00 PM
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.
Posted by: tristero | May 10, 2008 2:02 PM
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
Posted by: Cuttlefish, OM | May 10, 2008 2:11 PM
A Wordsworthesque wordsmith. Bravo!
Posted by: James F | May 10, 2008 2:15 PM
...
Also, Professor Myers, don't shrews and solenodons also have their own venom system?
Posted by: Stanton | May 10, 2008 2:18 PM
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
Posted by: James F | May 10, 2008 2:24 PM
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.
Posted by: amphiox | May 10, 2008 2:30 PM
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.
Posted by: Lago | May 10, 2008 2:33 PM
Say it with me now:
CONVERGENT EVOLUTION.
Posted by: Katharine | May 10, 2008 2:34 PM
Sigh, I don´t suppose either of those Nature articles have been made available online?
Posted by: plonkerinn | May 10, 2008 2:35 PM
Got it, not a chimera.
How about those poisonous spurs, thats hot!
Posted by: Mindcore | May 10, 2008 2:36 PM
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.
Posted by: CanadianChick | May 10, 2008 2:37 PM
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.
Posted by: Peter Ashby | May 10, 2008 2:42 PM
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?
Posted by: LARA | May 10, 2008 2:54 PM
I just happen to be wearing my Das Actionkino Schnabeltier t-shirt today in solidarity.
Posted by: Aaron Golas | May 10, 2008 3:02 PM
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"?
Posted by: heather | May 10, 2008 3:03 PM
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".
Posted by: Vaughn | May 10, 2008 3:06 PM
"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.
Posted by: Lago | May 10, 2008 3:06 PM
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.)
Posted by: Lynnai | May 10, 2008 3:07 PM
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.
Posted by: MIkeG | May 10, 2008 3:26 PM
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.
Posted by: D | May 10, 2008 3:49 PM
We see this more often in plants. Redwoods, Metasequoia (dawn Redwood), gingko, equisetom, etc..are known from the fossil records and go way back.
Posted by: raven | May 10, 2008 4:04 PM
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.
Posted by: robbrown | May 10, 2008 4:05 PM
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.
Posted by: Quidam | May 10, 2008 4:21 PM
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?
Posted by: Betz | May 10, 2008 4:29 PM
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.
Posted by: Katharine | May 10, 2008 4:42 PM
"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?
Posted by: Scott de B. | May 10, 2008 4:43 PM
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."
Posted by: Sili | May 10, 2008 4:46 PM
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...
Posted by: Lago | May 10, 2008 4:54 PM
@#49 Betz --
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:
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.
Posted by: Etha Williams | May 10, 2008 5:01 PM
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.
Posted by: MIkeG | May 10, 2008 5:33 PM
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.
Posted by: MIkeG | May 10, 2008 5:40 PM
@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!
Posted by: Lurker #753 | May 10, 2008 5:53 PM
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.
Posted by: valor | May 10, 2008 5:54 PM
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 :-)
Posted by: Bride of Shrek | May 10, 2008 6:07 PM
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.
Posted by: MIkeG | May 10, 2008 6:19 PM
Bride of Shrek, may I simply express my jealousy? I've never even seen one in a zoo.
Posted by: MIkeG | May 10, 2008 6:22 PM
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.
Posted by: mothra | May 10, 2008 6:39 PM
Thanks, MIkeG
That Wiki article does look helpful.
Posted by: valor | May 10, 2008 6:44 PM
Wait, wait, so the platypus *isn't* the crocoduck? Evolution is left defenseless! ;)
Posted by: miller | May 10, 2008 6:54 PM
"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.
Posted by: Lynnai | May 10, 2008 7:35 PM
@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.
Posted by: TomG | May 10, 2008 8:05 PM
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.
Posted by: Blind Squirrel FCD | May 10, 2008 9:44 PM
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.
Posted by: MIkeG | May 10, 2008 9:57 PM
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.
Posted by: sfs | May 10, 2008 10:34 PM
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.
Posted by: Rita Bennett | May 10, 2008 10:34 PM
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?'
Posted by: BadAunt | May 10, 2008 10:52 PM
@ 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.
Posted by: Betz | May 10, 2008 11:18 PM
True Christians (tm) excepted, as these are characteristically identified by their modest and ingratiating humility.