Archive May 2011

if pharyngeal slits turn into gills, why don’t humans have gills? Alison Campbell May 31


It seems that Intelligent Design advocates have challenged PZ Myers to answer ’10+1′ questions about evolutionary biology, while he’s on an upcoming visit to Glasgow. PZ’s published the list here. One in particular caught my eye, because it mentioned lungs (the subject of a recent post of my own), so I thought I’d have a crack at answering it myself.

9) If, as is often claimed by Darwinists, the pharyngeal pouches and ridges are indeed accurately thought of as vestigial gill slits (thus demonstrating our shared ancestry with fish), then why is it that the ‘gill-slit’ region in humans does not contain even partly developing slits or gills, and has no respiratory function? In fish, these structures are, quite literally, slits that form openings to allow water in and out of the internal gills that remove oxygen from the water. In human embryos, however, the pharyngeal pouches do not appear to be ‘old structures’ which have been reworked into ‘new structures’ (they do not develop into homologous structures such as lungs). Instead, the developmental fate of these locations includes a wide variety of structures which become part of the face, bones associated with the ear, facial expression muscles, the thymus, thyroid, and parathyroid glands (e.g. Manley and Capecchi, 1998).

Let’s get the really glaring error out of the way first. Our questioner says that pharyngeal pouches “do not develop into homologous structures such as lungs.” Bzzzzzzzt! Wrong! Lungs are not homologous to gill slits – they do not have anything approaching a common evolutionary history. I guess you could describe lungs & gills as analogous, because they are both involved in gas exchange, but that’s as far as it goes. Lungs formed as outpocketings from the gut, not from the pharynx.

Down to the meatier stuff. The questioner is happily conflating pharyngeal pouches with gill slits, presumably so that s/he can set up that ‘gills -> lungs’ strawman. Pharyngeal pouches are found in some form in all chordates, even if only during embryonic development. As the name suggests, they are outpocketings from the pharynx. But not all of them pierce the body wall, or function in gas exchange.  In cephalochordates like Branchiostoma (personally I find the old name Amphioxus more euphonious), the pouches become slits that pass through the pharynx wall & open into the surrounding body cavity (the coelom).  These structures do not function in gas exchange – this takes place across the thin epidermis that covers the animal’s body & lines its coelom (which is open to the sea). Instead, the pharyngeal slits act as a filter-feeding mechanism, trapping food particles from the current of water flowing over them. The same is true for sea squirts.

Yes, in fish the pharyngeal pouches go on to push through to the outside of the body, and the tissues between the ‘slits’ develop into the gill bars of bone or cartilage that support the delicate filaments of the gils themselves. Those gill bars are important, because we can trace their developmental fate, not just in fish but in frogs, reptiles, birds and mammals. And what do we find?

Jawless fish, aka agnathans - like lampreys – have mouths but (rather counterintuitively) no jaws. Juveniles are filter-feeders, just like Branchiostoma, but adult lampreys show vampiric tendences, latching onto passing fish with their toothy lips and rasping at the prey with a tooth-bearing tongue until they can suck at its blood. But embryological studies show that the first two sets of gill-bars in agnathans are homologous to the jaws of all other fish – they were co-opted for another function, a very long time ago indeed. The first set formed the ‘mandibular’ bones of the jaw, while the second is called the hyo-mandibular arch & helps to link a fish’s jaw to its skull. One explanation for this co-option is that it involved a change in Hox gene switching, opening up new ways of getting food. (A mutation, in other words. Which pretty much negates the tired old contention, revived in another of those 10+1 questions, that mutations are always harmful.)

And we can trace the fate of other sets of gill bars – and the associated circulatory loops – in frogs and reptiles, birds and mammals. The pharyngeal pouches are homologous to the various small glands that you find in the neck (thymus, thyroid, and parathyroid glands). The cartilage of trachea and larynx are ultimately derived from the gill bar tissues. And remember the hyomandibular arch in fish? It’s ended up as the stapes in your middle ear.

Oh yes, I mentioned the plumbing. In fish, each gill slit has an accompanying set of blood vessels (5 in most sharks – at Massey we used to dissect them out as part of first-year bio labs). Lewis Held (2009) comments that

Human embryos go to the trouble of making five pairs of aortic arches (which once sent blood to five pairs of gills) but then destroy two of them completely**. This Sisyphean stupidity only makes sense as a historical constraint: it must have been genetically easier to reconfigure the existing plumbing than to scrap it altogether and start afresh.

(** The remaining aortic arches become the vessels that take oxygenated blood to the lungs, head, and body.)

Lewis Held (2009) Quirks of human anatomy: an evo-devo look at the human body. Cambridge University Press. ISBN 978-0-511-59384-0 (e-book, Kindle edition)

the sarcastic fringeheads Alison Campbell May 30


Wouldn’t that make a great name for a band?

Rather to my surprise, I’ve discovered that ‘sarcastic fringeheads’ are actually…

… fish!

I heard this from the daughter when she came home from an evening of watching David Attenborough videos with some friends, & so of course I had to learn more. First up was hunting down the video, which you’ll find here, if my embedding doesn’t work. (I love listening to Attenborough’s voice – it’s got to the point where, when I’m reading one of his books, I can hear his voice speaking the words in my mind.) The first thing that struck me about that clip wasn’t the fringehead itself but the wonderful bed of waving brittlestar arms surrounding it. Just glorious! But the fish… belligerent, beautifully coloured… that amazing gaping set of ‘lips’… and my, what a mouthful of sharp pointy teeth they have! 


Perhaps fortunately for divers, these fish are quite small – around 30cm long. What they lack in size, they seem to make up for in sheer aggression. But why ‘sarcastic fringeheads’? We talked about it over dinner with friends last night, & one friend suggested that it might have something to do with that mouthful of teeth. After all, ‘sarcastic’ means ‘cutting’ (& not in a nice sense), and the word ‘sarcasm’ was originally derived from a Greek word with the literal meaning ‘to strip off the flesh’. And I suppose ‘fringeheads’ may have something to do with those amazing flaps of skin & flesh that male fringeheads can project around their gaping mouths, using them in mouth-to-mouth combat with neighbouring territory owners..

I still think it would be a good name for a band, though :-) No, wait, someone’s already used it for the title of an album. Rats.

why are some chickens white? Alison Campbell May 27

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Apparently this is a question that has been known to keep some biologists awake at night. (Can’t say I’m one of them; my insomnia is caused by other, equally pressing issues LOL)

Anyway, ERV has written a lovely post looking at this: apparently it’s all to do with metabolic pathways and endogenous retroviruses. Go over there & soak up the goodness :-)

(And sleep well.)

twisting the truth on vaccination Alison Campbell May 25


This ‘bad science’ letter popped up in the Waikato Times a couple of days ago. It was actually entitled “Democratic right”…

[A previous writer] condoned governmental blackmail in his letter in which he accused me of irresponsibility for defending the democratic right to choose whether to immunize or not. Does [he] know the MMR vaccine that is used in New Zealand is manufactured from aborted foetal tissue?

There are many parents who choose to avoid some vaccines for religious or philosophical reasons (for example, Catholics who oppose abortion) because the rubella virus in the vaccine is cultured on human diploid cells derived from human foetal tissue. I personally think that if more parents realized where the vaccine came from, they would not allow their child to be immunized.

Further, if [the previous writer], like me, had a sister who had a bad reaction to vaccination and who has suffered the effects of it all her life, he might think again. Also, a neighbour’s child who was a bright, alert baby, but after the second baby vaccine became dull-eyed, drooled at the mouth and hung her tongue. She is now an adult who has not married and is only capable of holding a mundane job.

Before labeling people irresponsible and denying them the rights of society, [the previous writer] should think again and see how he would feel if he were faced with any of the above.

First up, the MMR vaccine used here is NOT ‘manufactured from aborted foetal tissue’. No ‘foetal tissues’ are used in making this or any other vaccine. The writer does go on to say that  cells derived from foetal tissue are used – but these are cell lines that date back to the 1960s and 70s and have been grown in culture ever since then. They came from legal abortions, which were not performed for the purpose of obtaining these cells, and the use of these immortal cell lines hardly encourages abortion. (Those cells are like the HeLa cells used in cancer research and derived from tissue samples taken from Henrietta Lacks back in the 1950s during a biopsy for a cervical tumour. Henrietta’s story is told in The immortal cells life of Henrietta Lacks, by Rebecca Skloot – another one to add to my must-read list.)

While individuals may have personal ethical objections to the use of vaccines developed using these cells, it seems that the same is not true for the Catholic church itself if the folliowing statements from the US National Catholic Bioethics Centre are anything to go by:

There would seem to be no proper grounds for refusing immunization against dangerous contagious disease, for example, rubella, especially in light of the concern that we should all have for the health of our children, public health, and the common good” and “It should be obvious that vaccine use in these cases does not contribute directly to the practice of abortion since the reasons for having an abortion are not related to vaccine preparation.”

I don’t know why the ‘diploid’ bit is there, unless perhaps to raise the possibility of DNA contamination of the vaccines. If this did exist, and minute amounts of DNA were in the MMR (& I’m speaking hypothetically here) – it’s not going very far from the muscle tissue to which vaccination delivers it.

Doctors are well aware that vaccines are not entirely risk-free. (Before anyone jumps up and down about this statement, they should remember that NOTHING in life can be guaranteed risk-free.) However, these risks can be quantified. For measles, for example, the risk of harm from the vaccine is about 1 in one million; the risk of serious harm, including death, from measles itself is around 1 in one thousand – three orders of magnitude greater.

For rubella, (the focus of our letter), the foetus is most at risk, although adults occasionally suffer complications. For example, 58% of affected individuals have some degree of ‘sensorineural deafness); 43% develop eye abnormalities, including cataracts; 50% develop congenital heart disease. In comparison, the chances of a child having (eg) febrile convulsions following vaccination are between 4 in 10000 and 8 in 10000.

Yes, it’s devastating to have a child suffer genuine harm from a childhood vaccination, but it’s no less so for families whose children are harmed by a vaccine-preventable disease (& I’ve seen the effects in family members from my father’s generation and, indeed, in my own mother).

Our letter writer would seem to be suggesting that she’d prefer to see children exposed to a significant risk of permanent harm from the disease that the vaccine, with its much lower risks, is intended to avoid. Perhaps she would like to reconsider.

talking about exaptations Alison Campbell May 24

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During a lecture to our second-year evolutionary biology class I introduced the concept of exaptations: features that have evolved in one environmental context but which have been co-opted to fill a different role in a changed environment. This was in the context of swim bladders/lungs, which I’ll talk about in a minute, but right now I’m regretting not having read further through Lewis Held’s Quirks of human anatomy before the lecture, as he’s got a different, fascinating example (Held, 2009):

Darwin made an interesting observation about our fontanelles. He noted how lucky we are that these hinges were already in place (because of how skull bones grow) before they acquired the function of allowing our skull to deform during the tight squeeze of the birth process. in other words, mammalian sutures were "co-opted" as hominin hinges:

"The sutures in the skulls of young mammals have been advanced as a beautiful adaptation for adding parturition [birth]… but as sutures occur in the skulls of young birds and reptiles, which have only to escape from a broken egg, we may infer that this structure has arisen from the laws of growth, and has been taken advantage of in the parturition of the higher animals."

My example, lungs, was in the context of tetrapod evolution. There’s a rather nice series of fossils demonstrating the links between early amphibians and almost-as-early four-legged vertebrates, in this post by afarensis. That story also gives a nice example of the predictive power of evolutionary theory. Tiktaalik roseae was found because scientists working in that area knew that amphibians could be found in rocks of a particular age & early tetrapods in somewhat younger rocks. They predicted that an intermediate species might be found in rocks of intermediate age, identified a likely locality, went fossil hunting, and bingo!

Anyway, one of the big problems with life on land is that gas exchange becomes rather more complicated. While there’s much more oxygen in air than in water, getting it is in some ways more difficult. Gas exchange surfaces need to be moist, but gills or skin, for example, would dry out very quickly if exposed to the air for too long. And in any case gills are useless as a gas exchange surface in air – their fine filamentous structure must be supported by water or it collapses into a thick clumpy mass with relatively little surface area exposed to the ‘respiratory medium’ (shorthand for the oxygen-bearing air or water). And for an animal testing the air, as it were, half a lung is not going to be good enough.

Now, we know that lungs originated as outpocketings from the gut – they’re lined with the same endodermal tissues. The thing is, when did this happen and what sort of selection pressures might have been operating? The ‘when’ seems to have been a looong time ago, as lungs & lung derivatives – swim bladders – are found in all bony fish lineages, & bony fish first appear in the fossil record back in the Devonian. (It’s more likely that lungs evolved in the common ancestor of all those modern fish groups, than that they all evolved them independently.)

The current hypothesis for the origin of lungs is that they probably evolved in Devonian fish living in ponds or shallow lagoons. Geological evidence indicates that there were alternating wet & dry seasons back then &, just as today, during the dry weather water levels would drop & conditions in them would become hypoxic (low in oxygen). Fish able to gulp air at the surface, and sequester it somewhere in the gut, would be at a selective advantage in these conditions (& before someone comes along & says, this is just a just-so story, remember that there are modern fish able to do this, holding their gulped bubbles of air in the mouth or somewhere along the intestine, whence oxygen can diffuse into the bloodstream). Any increase in size of the bubble-holding part of the gut – which from the position of lungs/swim bladders in living species must have been in a ventral outpocketing from the foregut – would have been selected for, as would any increase in the capillary beds associated with the nascent lung.

(And of course, that has landed us with a whole lot of problems further down the line – because the paths of food and air must cross at the back of the pharynx, something that brings with it the ever-present risk of choking. One of the hallmarks of evolution is that it optimises, rather than producing perfection.)

Lewis Held (2009) Quirks of human anatomy: an evo-devo look at the human body. Cambridge University Press. ISBN 978-0-511-59384-0 (e-book, Kindle edition)

another weird science letter Alison Campbell May 23


This one seems to be firmly in the ‘nature good, man-made bad’ camp.

Doctors, drug companies and journalists alike refuse to acknowledge that what they manufacture, prescribe and pontiificate about is harmful to each and every human being. If children become poisoned, as reported [the writer is referring to a recent case where a child died after swallowing an adult's heart medication], then why should adults be less vulnerable? Certainly not. Simply more and more body cells are destroyed.

I’m sure those whose lives have been saved by modern pharmaceutical products (including antibiotics, anaesthetics, painkillers, and yes, chemotherapy) would disagree. Where chemo is concerned, doctors freely admit that the drugs are toxic – they have to be, to kill cancer cells. The oncologist must judge the treatment carefully to avoid killing too many healthy cells as well. (And yes, I know that statyement’s ripe for quote-mining!) And of course, dosage is important – the amount of a drug that can treat an adult ailment will quite likely be dangerous for a child.

Science can only succeed in making one form, whereas nature makes many forms (isomers).

I’m guessing that here our writer is referring to the fact that many molecules are chiral, whereby a very small change in the molecule’s physical form can have very large effects on its biological activity. However, he’s wrong on a couple of counts. First, chemists are quite capable of manufacturing more than one isomer of a particular chemical, and second – for chiral molecules anyway - living things utilise only one form of each molecule. What’s more, one ‘stereoisomer’ can be safely used by the body, while in some cases the other can be highly toxic – these days great care is taken during the manufacturing process to ensure that only the correct isomer is used in the final product.

Nature’s pure essential oils harmonise our cells; drugs, by contrast, being created synthetically increase disorder. .

Not quite sure about this ‘harmony/disorder’ thing.  Cells by their very nature are highly ‘ordered’, complex systems. OK, I’m sure an aromatherapy session is pleasant, relaxing, and improves one’s overall feeling of well-being. But more than that? I notice that essential oils are pushed by Mercola as having ‘significant therapeutic benefits’, which by itself makes me cautious :-) But anyway. This site advises that they shouldn’t be taken internally, which would rather tend to limit their effectiveness on internal ailments. And some are certainly not without their side effects:a 2007 study of gynecomastia (breast development) in prepubertal boys found that in some cases this could be traced to the use of lavender and tea-tree oils.

Show me where manmade intervention is as good as nature provides.

Ever taken an aspirin? The active principle in aspirin was originally obtained from willow bark. Modern methods of producing it mean that dosage can be standardised & the drug used more effectively. Nor is ‘nature’ this gentle, caring, universally beneficent thing. There are many entirely natural substances that will kill you very dead – including ricin, from the castor oil bean: the toxin of choice used to kill Georgi Markov back in 1978. (And – I can’t resist – won’t someone warn people about dihydrogen monoxide?)

Ignorance and arrogance play big parts in the lack of acknowledgement of the powers of nature, in the interest of money-making benefits rather than for health.

Any doctor who’s seen a patient die of an intractable ‘superbug’ infection, or from cancer that’s advanced beyond the ability of oncologists to offer anything more than palliative care, is all too aware of the ‘powers of nature’. They don’t see why nature should always simply run its course – bear in mind that that 200 years ago, most people could expect to live only around 40 years. Modern medical and pharmaceutical advances have done a lot to change that.

another lovely biological image Alison Campbell May 22

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Grant & I have something of an ongoing friendly competition to come up with stunning & unusual biological images. Here, via PZ (as usual!) & The Node is my latest offering:


It’s a confocal microscope image of a squid embryo. The reddish areas are neural tissue (mmmm, braaaainzz) & each of those fluorescent green speckles is a tuft of cilia. (I wouldn’t have known that stuff but Sven DiMilo, one of PZ’s ‘regulars’, kindly explained it.)

Just lovely :-)

Your turn, Grant!

waiter, there’s a fish in my cucumber! Alison Campbell May 19

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My sea cucumber, that is.

was going to write something full of snark about the current brouhaha around predictions that the world is going to end on May 21st. But Darcy has beaten me to it! So instead (from the Echinoblog, and via PZ) I offer you… [drumroll]…  the sea cucumber with fish residing in its nether regions!


 (Photo by Claude Rives from Fishbase)

 Isn’t that a rather wonderful image?

Sea cucumbers (holothurians) are echinoderms: they’re closely related to starfish, sea urchins, and brittlestars (plus a couple of other, less familiar, groups). Like all echinoderms they have a body plan that’s unique in the animal kingdom: as adults they are radially symmetrical (more precisely, they are pentaradiate, with 5 axes of symmetry) and move around by means of a hydraulic system that powers 5 rows of tube feet running down the body – or along the arms, if you’re a starfish. In a sea cucumber that symmetry part is a bit obscured by the fact that the animal’s body is elongated, but it’s still there. They don’t have a circulatory system either; instead, their body cavity is pretty much open - in fact the Echinoblog describes them as ‘bags of water & guts’ – so their organs are awash in a body fluid that circulates nutrients and wastes.

And their guts are often awash (although that might not be the best word) with fish…

 The fish you see peeking out of the back end of that rather beautiful holothuroid is a pearlfish (Carapus sp.), and the relationship, although it looks uncomfortable, is apparently commensal – the fish gains shelter and the cucumber seems unharmed (& also unbothered -there really is quite a lot of room in there, in a large cucumber, & some of them can grow up to 600mm or so long). The relationship between fish and host isn’t always so benign. Parmentier & Vandewalle (2005) point out that fish in the genus Encheliophis actually eat the host’s gonads!!

It’s odd that the fish can get in there in the first place, actually, as sea cucumbers have a most unusual anti-predator defence system that you would surely expect to be triggered by having a fish nosing around one’s rear end :-) Nudged by a would-be predator, a holothurian points its anus in the direction of the potential threat – & squirts out part of its gut! Or, more precisely, the ‘cuverian tubules’ that make up part of the respiratory trees, which in turn are attached to the gut. Understandably the predator is rather confused by this, and also rather gummed up as the tubules lengthen and get very sticky when expelled, so the cucumber may have a chance to make a (slow) escape. When I first heard about this trick, I was told that the tubules were actually eaten by the predator, but apparently this isn’t so as they are rather toxic.

The cucumber, incidentally, isn’t mortally injured by the loss of part of its guts: the missing bits regenerate & life goes on as usual, with the cucumber using its oral tentacles to filter food particles from seawater or sand & then carefully licking each tentacle clean. And the pearlfish scout around for fresh homes, finding each host’s cloaca by sensing the stream of water expelled from the anus as the cucumber respires. (Remember, its gas exchange organs – the ‘respiratory trees’ – are connected to its hindgut. These are strange animals indeed.)


Rats, I forgot the reference!!

E.Parmentier & P.Vandewalle (2005) Further insight on carapid-holothuroid relationships. Marine Biology  146(3): 455-465, DOI: 10.1007/s00227-004-1467-7

pink – not for boys? Alison Campbell May 10

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Over on Sciblogs, Michael Edmonds has written about a report from the US, wherein a mother is castigated for putting (wait for it!) pink nailpolish on her son’s toenails. Apparently the response in some quarters has been one of Shock, horror! The poor child will be scarred for life.

Unfortunately there’s been a certain amount of rather shaky ‘evolutionary psychology’ research that purports to explain differences in colour preference between the genders in terms of women being the gatherers & needing to be able to tell when the berries are ripe… Michael’s post reminded me that I’d written about this issue myself, a while ago now. And also that the inimitable Ben Goldacre had addressed the whole gender/colour ‘preferences’ thing himself. His take was so good that I’ve pasted the best bits below (with emphasis added in bold), as it’s worth sharing again :-)

But is colour preference cultural or genetic? Well. The ’girls preferring pink’ thing is not set in stone, and in fact there are good reasons to suspect it is culturally determined. I have always been led to believe by my father — the toughest man in the world — that pink is the correct colour for mens’ shirts. In fact until very recently blue was actively considered soft and girly, while boys wore pink, a tempered form of fierce, dramatic red.

There is no reason why you should take my word for this. Back in the days when ladies had a home journal (in 1918) the Ladies Home Journal wrote: ’There has been a great diversity of opinion on the subject, but the generally accepted rule is pink for the boy and blue for the girl. The reason is that pink being a more decided and stronger color is more suitable for the boy, while blue, which is more delicate and dainty, is prettier for the girl.’

The Sunday Sentinel in 1914 told American mothers: ’If you like the color note on the little one’s garments, use pink for the boy and blue for the girl, if you are a follower of convention.’ Some sources suggest it wasn’t until the 1940s that the modern gender associations of girly pink became universally accepted. Pink is, therefore, perhaps not biologically girly. Boys who were raised in pink frilly dresses went down mines and fought in World War 2. Clothing conventions do change over time.

But within this study, was the preference stable across cultures? Well no, not even in this experiment, where they had some Chinese test subjects too. For these participants, not only were the differences in the overlapping curves not so extreme; but the favourite colours were a kind of red for boys and a bit pinker for girls (not blue); and they had more of a red preference overall. Red, you see, is a lucky colour in contemporary Chinese culture.

why geologists are wrong, wrong, wrong! about the age of the earth Alison Campbell May 06


I came across the following diagram on Peter Bowditch’s wonderful The Millenium Project. Like him, I hope it’s a poe; but nonetheless, I find it has a certain dreadful fascination. Who knew that geologists could get it so wrong?

proving atheists wrong with science.jpg

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