Friday 28 June 2013

Biological Systems: Is Redundancy Redundant?

The term redundancy is often used to describe two or more processes in biological systems that appear to do the same job. The term has been borrowed from Information Theory. The definition in Wikipedia is as useful as any:
Redundancy in information theory is the number of bits used to transmit a message minus the number of bits of actual information in the message. Informally, it is the amount of wasted "space" used to transmit certain data.
I have never been comfortable with the term in biological systems except in discussions on signalling systems (endocrine, autocrine, paracrine, intracrine) where it can be used in its proper, Information Theory, sense. My qualms on using it for biochemical pathways and membrane transport systems, for example, are that it has implications of a mechanism being present but not needed. I have argued in the past that parallel pathways and different transport mechanisms carrying the same substrate are better described as safety mechanisms (belt-and-braces adaptations) or as systems that may be used in some circumstances and not others.

The other problem in using the term is that it can be confused with redundancy in the evolutionary sense, a vestigial character for example. I sometimes think we should leave the term in its more usual English meaning of superfluous in the hands of human resource departments, those parasitic forms of life, to apply to themselves. Auto-redundancy in these anti-personnel departments would do more than a little to aid economic recovery — and benefit science, technology and engineering.

The twitching of my ears and muscular contractions in other parts of my anatomy at hearing the term (along with ‘model organism’, ‘model system’ and the like) appear more and more to be justified as mechanisms are investigated in greater depth than the appearance of blots on gels.

A recent paper in Proceedings of the Royal Society* by Zoe Dumas, Adin Ross-Gillespie and Rolf K├╝mmerli sums up in its title the dangers of using the term willy-nilly: Switching between apparently redundant iron-uptake mechanisms benefit bacteria in changeable environments. I can do no better than to quote from the abstract:
Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores—the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores…
So, how many apparently redundant mechanisms can really be described as such? Perhaps we really should confine it to its proper use in signalling systems where redundancy in the message decreases the error in transmission.

Peaker, M. 1992. Chemical signalling systems: the rules of the game. Journal of Endocrinology 135 1-4
Proceedings of the Royal Society B 7 August 2013 vol. 280 no. 1764 20131055
Sir Barry Cross’s loudly whispered description in the early 1980s of the personnel department of the old Agricultural Research Council (later AFRC, now BBSRC)

Sunday 23 June 2013

Donors of Reptiles to London Zoo 1914/15: 8. Herbert Tomlin Pollitt

Again, and nearing the end of this series of posts, this is what Clin Keeling wrote in A Short History of British Reptile Keeping:

H. Pollit of 7 Grosvenor Road, Handsworth, Birmingham, gave an Alligator, an Eyed Lizard and a European Pond Tortoise…

Thanks to a search of the 1911 Census, a family history on and the keeper of that history, Any Pollitt, I have identified this ‘H. Pollit’ as Herbert Tomlin Pollitt. He was born in 1897 in Irlam, Lancashire. In 1911, aged 13, he was living at the address shown in the Zoo’s records. His father, a chemist, was manager of a soap works; he worked for Lever Brothers (now Unilever).

Herbert had ‘a very colourful life’. In 1917 he was commissioned 2nd Lieutenant from the Indian Army’s Cadet College at Quetta (now in Pakistan). The Cadet College occupied the buildings of the famous Staff College which was closed for the duration of the war. By the end of the war it appears he was with 20th Deccan Horse, an Indian Army cavalry regiment (renowned for its charge on the Somme in 1916) on the western front.

He became a garage owner (authorised Morris dealer) in Birmingham, and is shown as living on a farm near Droitwich. Thrice-married, he was killed, along with a son from his second marriage and a son from his third marriage, in November 1965, aged 68.

So here we do seem to have somebody who may have given his reptiles to London Zoo before joining the army. We do not know if he retained any interest in animals after the war or at the farm where he lived near Droitwich.

We also do not know where he got his reptiles in the first place. It seems unlikely that they come from his father’s travels For Lever Brothers since one was North American and the others European. However, I cannot help wondering if they came from a local source. Clin Keeling mentions C.R. Walker from “The Vivarium”, West Bromwich (I will deal with him in a later post) as a donor of reptiles to London Zoo over this period. Handsworth is adjacent to West Bromwich. Was there a connexion?

Tuesday 18 June 2013

Blue Poison-Dart Frog: The Times Gets It All Wrong

The Times really should check its sources and material before publication. Today’s edition has a short article that states:

British scientists have successfully bred a rare species of frog that contains enough poison to kill up to ten adults. The blue poison dart frog, which is 2.5cm long, is found in the tropical forests of Costa Rica and Brazil. Experts at Walford and North Shropshire College have successfully bred one in their laboratory…

What a load of cock. Where did The Times get such an inaccurate story?

The blue poison dart frog was originally described as Dendrobates azureus. It was discovered in 1968 in mountainous island in the Sipaliwini savanna of Suriname. It was named by its discoverer (Hoogmoed) in 1969. He writes:

In 1970 I returned to the Sipaliwini savanna on another expedition and at that time I collected 10 specimens of D. azureus from the Vier Gebroeders forest island, and transported them alive to Holland, where they formed the basis of the first, and only legal, breeding colony of D. azureus. All other colonies were established with smuggled specimens, from which the present specimens in captivity are descendants1.

Private breeders in the Netherlands and Germany soon began to breed these frogs and they entered the open market. Some zoos (Edinburgh was one) were also keen to breed them because of reports that their habitat was threatened by fire. In short, D. azureus was, for a short time, treated as an endangered species.

I bought adults and tadpoles from Dutch breeders in the early 1990s and the late Bob Davies and I bred them. They are now commonly kept and bred in captivity throughout the world and there is no justification whatsoever in the claim published in The Times. Indeed, an quick search shows them available at £60 each from a British dealer. As the IUCN website3 says:

This species breeds easily in captivity, and is found in zoos around the world.

Having seen these frogs alongside coloured forms of Dendrobates tinctorius, the thought of many of us was that they were a local form of D. tinctorius. Other than in colour they resembled D. tinctorius and there was no evidence that tinctorius and azureus were sympatric. This suspicion was confirmed in 2006: D. azureus was demoted to a junior synonym of D. tinctorius (summary in 2).

All the information anybody needs, from taxonomy to distribution, is readily available from the IUCN website where D.tinctorius rates ‘least concern’3.

So, here’s one we bred earlier:

The reason for my writing about this claim here is to highlight a common and growing problem. Zoos and wildlife collections are forever putting out press statements that they have bred such-and-such and that it is ‘endangered’. Such claims are rarely true and even when it is correct that the species in question is endangered, or in some other less than safe category in the wild, there are often so many in captivity that zoos do not know what to do with them. Not only do such silly or trivial claims play straight into the hands of members the anti-zoo lobby who know a false claim when they see one but detract from the hard-earned achievements of those involved in ex-situ conservation.

I now expect to see reports that such and such an organisation has bred axolotls — critically endangered in the wild. I shall probably read the report while drinking coffee in Dobbie’s Garden Centre, yards away from tanks containing axolotls at £22 each.

Wednesday 12 June 2013

Donors of Reptiles to London Zoo 1914/15: 7. Bernard Tucker and William Waldegrave

Again, in this series of posts, this is what Clin Keeling wrote in A Short History of British Reptile Keeping:

Mr. W.B. Tucker of Hillside, Harrow on the Hill, Middlesex, got rid of a Brazilian Tortoise, a Spanish Terrapin and a Scorpion Mud Turtle (this latter one of the Box Turtles), and I was intrigued to discover that a few months later he sent, from Chewton House, Chewton Mendip, near Bath, two Radiated Tortoises, a Rough Terrapin (!) and three more Scorpion Muds on behalf of Lord Chewton. Was the latter, I cannot help wondering, an earlybut self-effacing practical herpetologist who had persuaded Mr. Tucker, who he knew to be similarly-minded, to come westwards in order to look after his collection - some surplus of which he decided to donate to the Zoological Society of London?

A few searches soon showed that somewhere there has occurred a transposition in the initials. W.B. Tucker is, in fact, B.W. Tucker — Bernard Tucker (1901-1950), the renowned ornithologist and lecturer in Zoology at Oxford. All the facts fit: educated at Harrow (Hillside was, apparently, one of the smaller houses at Harrow); family connexion with Chewton Mendip; a keeper of reptiles and amphibians in his rooms at Oxford.

Bernard Tucker

An account of Bernard William Tucker’s life was written by David Lack. Originally published in Ibis in 1951 it was reproduced in his book, Enjoying Ornithology (Methuen, 1965). I can do no better than to quote from it:

With the death of Bernard William Tucker on 19th December 1950 after a long illness, British ornithology loses it central figure. This position Tucker had come to fill, in characteristically unobtrusive fashion, partly through the width of his interests, which ranged from the identification of rare waders to the physiology of feather-growth, and particularly through his varied services to ornithology. He was Reader in Ornithology at Oxford University, Editor of British Birds, a former Vice-President of the British Ornithologists’ Union, and Vice-Chairman of the British Trust for Ornithology. 
Born on 22nd January 1901, at Northaw in Hertfordshire, Tucker spent most of his boyhood at Chewton Mendip in Somerset; and his first publication was on the birds round Chewton Mendip in the report of the Wells Natural History and Archaeological Society in 1918. He was educated at Harrow School, where he won the Lord Claud Hamilton Biology Prize in 1918 and the William Roundell Leaving Scholarship in 1919. He went up to Oxford in 1919 with a demyship (senior scholarship) at Magdalen College, and obtained 1st class honours in Zoology in 1923. He then obtained the Oxford scholarship to the Stazione Zoologica at Naples, where he worked on parasitism in crustacea for a year, paying later brief visits to Naples in 1925, 1927 and 1928. At Naples, also, he met his future wife, Gladys Allen, whom he married in July 1925. In the same year he was appointed a Demonstrator in the Zoological Laboratory at Cambridge, Professor Stanley Gardiner’s intention being that he should fill Gadow’s place as lecturer in vertebrate anatomy. When Gadow unexpectedly postponed his retirement, Tucker in 1926 returned to Oxford under Professor Goodrich, and he became a University Demonstrator and Lecturer in Zoology and Comparative Anatomy in the following year. This post he held for the rest of his life, becoming Browne Research Fellow of the Queen’s College 1944-47 and Reader in Ornithology in 1946.
Tucker once told me that he differed from most ornithologists in that he did not develop an overriding interest in birds until unusually late, about his eighteenth year. At school, botany had been a major interest, and as an undergraduate he was noted for the variety of reptiles and amphibia which he kept in vivaria in his rooms…. 
In the zoology department at Oxford, Tucker lectured mainly on the vertebrates, including of course the birds, and he was one of the first in Britain to supplement the orthodox lectures on anatomy with others on habits, including migration. He was noted for his skill both in dissection and in anatomical diagrams, some of the latter being published in De Beer’s Vertebrate Zoology, which became a standard textbook for students… 
Tucker has had an extremely important influence on British ornithology in three different ways, through his work with local ornithological societies, through his work on field characters, particularly as published in the Handbook of British Birds, and through his work for the Edward Grey Institute at Oxford… 
In B.T.O. affairs, however, Tucker’s greatest service was at Oxford, for he, more than anyone else, was responsible for getting University support for the Institute…

In the obituary, Lack states that Tucker’s original publications on birds are few and unimportant. He does not mention that Tucker dissected the head of London Zoo’s last Thylacine after its death in 1931*. Typically, I suspect, he did not publish this study but his notes and the head are in the university’s museum at Oxford.

Tucker would have been 13 when his gave his chelonians to London Zoo. Were they too difficult to keep at school?

Viscount Chewton then was William Edward Seymour Waldegrave (1882-1933). He later succeeded to the title, 10th Earl Waldegrave. He was the son of the 9th Earl (William Frederick Waldegrave) and Mary Dorothea Palmer. The family seat is at Chewton Mendip, where Bernard Tucker spent his boyhood. Waldegrave died, unmarried, at the age of 50. He became a Fellow of the Zoological Society in 1913 (aged 31). One can only assume that Tucker and Waldegrave developed a common interest in reptiles, especially chelonians, at Chewton Mendip. Whether Waldegrave continued his interest beyond the 1st World War, I do not know.


Tuesday 11 June 2013

Birds and Light Pollution: Hong Kong at Night

A correspondent in Hong Kong writes:
If you are in the centre of Causeway Bay at the Sogo crossing around 9pm it is dark, but swallows are still feeding by hunting insects that are attracted to the large illuminated advertising hoardings. So yes they are still feeding and getting the extra food while their less urbanised relatives sleep.

Thursday 6 June 2013

Blackbirds and Light Pollution. A Man and his iPhone App at Dusk and Dawn

Passers by may have thought it a little odd. It is not every day they see a man crouched under bushes in the garden at dusk clutching an iphone. The reason for this madness was that I was intrigued by a paper* in Proc. Roy. Soc. on the effect of artificial light at night on reproduction in birds.

When I first saw the title my immediate thought was that there was nothing new. Since Rowan described what happened to starlings under London street lights in 1938, I thought I would be reading of something very similar. However, this new paper is concerned not with the typical levels of light that are known to advance reproduction in photoperiodic birds but with what happens with the low light intensities present in urban environments at night. First of all, they measured the intensity of light at night in urban and rural environments and then exposed blackbirds (Turdus merula) from cities or forests to either darkness or the low intensities typical of an urban environment at night. In short, the reproductive system developed earlier, and moulting occurred sooner, in birds exposed to low-intensity light (only 0.3 lux) at night. The authors concluded that light pollution is having an effect.

But then I began to worry. Is there something special about the blackbird? On those very early mornings when I had to set up for the airport with virtually no light in the sky, I often disturbed blackbirds already up and looking for worms in the garden. No other birds were active at that time. So, is the whole array of garden birds affected by the light pollution: chaffinches, house sparrows, greenfinches, starlings etc?

Then I began to wonder how is the low intensity of light perceived. Most birds here sleep with the heads tucked under their wings, some, the wren for example, in opaque nests. Would even extraocular light receptors be exposed? Do the birds wake at intervals to see if it is light enough to feed? And does even the low light then act through the usual photoperiodic channels?

That’s why I have crawling around the garden with my iphone. It has the LuxMeter app and that is showing me what the light intensities are when birds are active. But then I realised that in large parts of the northern hemisphere, including here in the West of Scotland, it never really gets dark in the summer, so that any effect of artificial light pollution could only be exerted in the short winter nights.

My (nearly) final thought was what happens to birds that are classically considered to be non-photoperiodic (like the estrildids in the tropics) in light-polluted cities. Do birds in the cities there have longer periods of activity and feeding and is there any other physiological effect?

And, really finally, is there any effect of the moon (0.25 lux on a clear night at full moon)?

*Artificial light at night advances avian reproductive physiology. Dominoni, D, Quetting, M Partecke, J. 2013. Proc. R. Soc. B 280, 20123017.