Journal Prices: How Science and Science Funding Lose Out

A few weeks ago a paper in Proceedings of the National Academy of Sciences of the USA* hit the headlines^†. It compared the cost of journal ‘bundles’ sold by ‘for-profit’ and ‘non-profit’ publishers to university libraries in the USA, under confidential terms revealed only by freedom of information requests to state-funded institutions. Not surprisingly the commercial publishers charged more for their bundles of journals. However, the size of the bundles from different publishers obviously varied. In order to get an idea of value for money, the authors then used the citation rating of a journal to obtain the price per citation for each bundle. Not surprisingly, the cost/citation was higher for journals bought from commercial publishers than from ‘nonprofits’. They must be higher since that is why commercial publishers are in business; they are not charities.

However, in using citation indices at all, the authors sadly scored an own-goal. Citation, as a measure of scientific worth, is utterly corrosive to scientific worth. I will not repeat the old arguments here since David Colquhoun’s Improbable Science Blog^‡ continues to do a fine demolition job.

In using citation indices at all, the authors of the PNAS paper provide ammunition to the commercial publishers. They can continue to extract money from publicly-funded science while researchers feel compelled by peer or institutional personnel policies to submit papers to journals with a high impact factor. Some commercial publishers have become highly skilled at recruiting editors (usually working at least in part in their employer’s time) and editorial boards who work in popular and active, i.e. inherently highly citable, fields. A successful journal in citation terms can therefore be a moneyspinner.

The ‘nonprofit’ publisher can also be a misnomer. University presses and society journals may also be run for profit, in fact ones I have been associated with were and still are. Journal profits are used to fund other society activities like travel grants and scholarships. In Britain, journals are often set up as subsidiary trading companies covenanting profits to their parent society, thereby preserving the charitable status of the society and avoiding corporation tax on their profits. The fact that society journals do not sell for as much as commercially-published journals can probably be attributed to a lack of marketing expertise (i.e. brass neck) and general commercial nous than to a desire to keep prices low. Open publishing is as welcome to those societies that rely on journal profits to sustain their activities as it is to commercial publishers. An irony of the article in PNAS is that to see it you have to pay for it!

Until I retired I was closely involved in deciding what money should be spent on library subscriptions. The first rule in dealing with publishers is never let a librarian have any role other than in providing data. Librarians just hate to discontinue the run of a journal. The second rule is monitor usage of current journals. The third rule is to threaten to cancel a whole bundle and do so if the price asked does not fall; the price asked soon falls. The calculation we used in deciding whether to cancel other than the obviously key journals was: would it be cheaper to get the required copies of articles from the British Library than buy the journal. In this way, savings on journals could be, and was, spent employing and equipping scientists.

The PNAS article draws attention to only part of the story. Allowing publishers to charge exorbitant prices to download old articles, sometimes more than 50 years old, is an absolute rip-off. ‘Nonprofit’ scientific societies that allow commercial publishers to handle their journal sales are as guilty as the rest in this respect. 

So, until scientists stop chasing citations, until action is taken to stop publishers charging excessively for old articles, until scientists stop providing commercial publishers with their own and their employer’s services for nothing and until libraries stop buying their wares the publishers will continue to ‘gouge’^†† science and science funders.

Fully open access, to publishing and reading of past works as well as present, must be the goal. And if that means changes to copyright law then get on with changing it. The PNAS paper at least shows ‘market failure’ that catch all trigger for government intervention. Action This Day is not even soon enough.

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* Bergstrom T C, Courant P N, McAfee, R P, Williams M A. 2014. Evaluating big deal journal bundles. Proceedings of the National Academy of Sciences of the USA , early edition doi:10.1073/pnas.1403006111

† Article in The Guardian:  http://bit.ly/1jvrLaU

‡ http://www.dcscience.net/?p=6636

†† employing the North American term, as in Jerry Coyne’s Blog at Why Evolution is True:
http://bit.ly/1nUeQQM

Abominable Snowman: Yetis from The Long Walk to Bear mtDNA

The recent paper on genetic analysis of hair samples from possible unknown species, brought back memories of the hunt for the  ‘abominable snowman’ or ‘yeti’ in the 1950s. For I was born within sight of ‘Cloud House’ in Sandiacre, Derbyshire (but on the Nottinghamshire side of the border across the River Erewash) which became the home sometime in the 1950s of Slavomir Rawicz, author of The Long Walk. Rawicz said he had seen such creatures while crossing the Himalayas in his tale of escaping from a Soviet camp and walking to freedom in India. To schoolboys in Stapleford, and probably to a greater extent to those in Sandiacre, whom we never met since they went to different county schools, it could only be a matter of time before somebody discovered what the beast was. With a celebrity author on the doorstep it could not be anything else.

Over the years, we have been disappointed. Lead after lead brought false hope and no convincing evidence. We could not stay in our 1950s state of superior knowledge for long (It shouldn’t be called the abominable snowman, the proper name is yeti, we would proclaim in the playground).

The yeti is where one set of myths and legends meets another set of myths and legends. The first set is about The Long Walk itself as I discovered a short while ago when I remembered Slavomir Rawicz and wondered what had happened to him (he died in 2004). I read the book at the age of 13 when the Companion Book Club edition arrived in the post. I was completely unaware his book had come under attack for being a fabrication (even allowing for journalistic licence on the part of the ghost writer, Ronald Downing of the Daily Mail, the newspaper which had funded a 1954 expedition to find the yeti). A number of reviewers of the book were highly sceptical at the time of publication and the intensity of investigation and speculation increased markedly over the past ten years or so. I have read numerous websites and Linda Willis’s book, Looking for Mr Smith, published in 2010, which attempted to find all the available evidence. Emerging records from Poland and Russia appeared to indicate that Rawicz could not have walked all the way from Siberia to India. Then other Polish émigrés in Britain claimed that they had made the walk and that Rawicz had not. But the records, if correct, appeared to rule these claims out as well.

Having read the available information, my view is that the story is an amalgam of the tribulations of Polish prisoners who escaped or who were released after Stalin’s amnesty in 1941 and then made their way from the USSR to join General Anders’s army which gathered at Pahlevi in Persia before going on to Palestine and to fight as Polish II Corps alongside the British Eighth Army in Italy. Surviving fragments of evidence suggest that some may indeed have walked from Siberia to India. Conversations between Anders’s troops on what happened to groups and individuals after they came together at Pahlevi could have provided the basis for such an amalgamation into one story. I also have the feeling that while Rawicz was named as the author, he may have been writing on behalf of a group of individuals, some of whom could not be named because of possible danger to family and friends left behind the Iron Curtain, and writing to ensure that the story of the horrors the Poles faced in Stalin’s USSR and their escape to fight for freedom would not be forgotten. Rawicz himself though in numerous interviews and correspondence defended his book to the last. Whether the real truth will ever be discovered I do not know. However, for the present story, the connection with the yeti is of interest. This is where the first set of myths and legends meets the second.

From some reports I have read, in January 1954 the Daily Mail published an article describing Rawicz’s encounter with yetis and that Downing then went to see him at home near Nottingham in order follow the story up; out of that meeting came The Long Walk. However, I have also seen that the January 1954 article was written by Downing (The Snowman: The Strangest Story Yet, Daily Mail, 7 January). How Rawicz’s yeti story came to be in the newspapers at all I do not know, and none of those who have avidly researched the veracity of The Long Walk seem to have looked into what I see as an important element in the story of how the book came to be written (I have not seen the early newspaper articles but would like to hear from someone who has). This is what Linda Willis wrote about the initial contact between Rawicz and Downing:

It was during 1954, with the increasing interest in Mount Everest, that word trickled down through contacts, either in the field of journalism or through returned servicemen, that there was someone living in the English Midlands who had been through an incredible adventure, including sightings of abominable snowmen.

If it was Downing's story that appeared on 7 January 1954, then it would have been during 1953, not 1954, that 'word trickled down'. That, however, gets us no nearer to determining what Rawicz’s motives were in seeking or accepting publicity for his claimed sighting of yetis.

In view of the doubts about Rawicz’s book, did he really see some animals that he could not identify himself at some stage in his travels? If he had not then he was obviously only too willing to perpetuate the mischief since a young friend of the family in one of the online discussions states that Rawicz gave him a sketch of the creatures. On the back was Rawicz’s signature and the inscription ‘Observed in the spring of 1942’.

So I turn from the continuing debate, with its mixture of real historical researchers and conspiracy theorists, on the Long Walk and Rawicz to consider real evidence in ‘cryptozoology’, that mixture of epi-zoology, psychology, anthropology and its own conspiracy theories I usually ignore.

The new properly-published genetic evidence is from mitochondrial DNA extracted from hair samples. Short sequences in a highly conserved gene from two samples of ‘yeti’ hair, one from Ladakh (golden-brown in colour) and one from Bhutan (reddish-brown), showed a 100% match to DNA recovered from a Pleistocene fossil of Ursus maritimus, the Polar Bear, but not with examples of modern polar bears. The authors consider three possibilities to explain the match: ‘a previously unrecognized bear species, colour variants of U. maritimus, or U. arctos [Brown Bear]/U. maritimus hybrids’. Hybridization is known between modern Polar and Brown bears in the wild and in captivity. The authors do not appear to have considered any involvement of the Himalayan Black Bear (Ursus thibetanus) in the mix which I find a little odd since they note that the hunter who shot the specimen in Ladakh noted that its kind ‘behave more aggressively towards humans than known indigenous bear species’ a characteristic of U. thibetanus (as well as of U. maritimus) compared with U. arctos.

The preliminary evidence suggests that a bear, with the strong possibility of an ancient polar bear as a maternal ancestor, accounts at least in part, and perhaps entirely, for the ‘yeti’.

This photograph of an American Black Bear (Ursus americanus) standing upright shows how easily a bear at a distance could be mistaken for a large humanoid primate, particularly if its head were pointed downwards while feeding on berries, for example. From George Jennison’s Natural History: Animals. London: Black. 1929

The thought also struck me last year when reading the brilliant biography of the physiologist, Griffith Pugh, Everest. The First Ascent, by his daughter Harriet Tuckey, that some sightings of humanoid animals by travellers in the Himalayas may have been not just humanoid but human. Tuckey wrote that in January 1961, a strange man walked into base camp at Mingbo (15000 ft, 4600 m). He was small, slight, barefoot and wearing only a turban, short jacket, cotton trousers and a shirt. He spent nights sheltered under a rock at temperatures below -10°C. He also had the curious habit of eating glass; microscope slides and pipettes preferred. It turned out that Man Badhur was a carpenter, and had come to the Mingbo Valley on a pilgrimage, the result of a religious revelation. Pugh who was fascinated by this pilgrim’s appearance made many physiological observations (published in 1963) to determine how Man Badhur survived the cold and, moreover, avoided frostbite.

However, my point is that perhaps Man Badhur was not a sole example of human animals walking and living off the land in the Himalayas. Such holy men could well appear at a distance to be some strange humanoid creature depending on what they were wearing.

In this post I have touched on myths and legends, from The Long Walk to the yeti. But I am still intrigued by Slavomir Rawicz’s description of an encounter with the latter. Was it him? Was it somebody else who had then told the story in Anders’s Army? Or was he seeking publicity for himself or the cause of exposing the foulness of Stalin’s USSR and just cashing in on the zeitgeist of all things Everest and the Himalayas in Britain after its first ascent on the eve of the Coronation in 1953? I just do not know.

Away from myths and legends, the scientific interest now lies in sorting out just what the bears of the Himalayas are and where they came from.

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Genetic Analysis

Sykes, B C, Mullis, R A, Hagenmuller, C, Melton T W, Sartori M. 2014. Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates. Proceedings of the Royal Society B 281, 20140161

The Long Walk

Books

Rawicz S. 1956. The Long Walk: The True Story of a Trek to Freedom. London: Constable. (This is the reference to the 1st edition)

Willis L. 2010. Looking for Mr Smith. New York: Skyhorse

Websites

http://www.mikaelstrandberg.com

http://www.theguardian.com/news/2004/may/05/guardianobituaries

http://www.telegraph.co.uk/news/obituaries/10158049/Witold-Glinski.html

http://www.nottinghampost.com/Slavomir-s-epic-tale-survival-reaches-big-screen/story-12165072-detail/story.html

http://zs.vpweb.com/The-Long-Walk-Mysteries.html

http://archive.spectator.co.uk/article/13th-july-1956/13/a-st-sunday-the-long-walk-by-slavomir-rawicz-was-d

https://groups.yahoo.com/neo/groups/tlw1941/conversations/topics/132
http://frontiersofzoology.blogspot.co.uk/2012/02/return-to-long-walk.html

Griffith Pugh

Tuckey H, 2013. Everest. The First Ascent. The Untold Story of Griffith Pugh, The Man Who Made It Possible. London: Random House

Pugh L G C E. 1963. Tolerance to extreme cold in a Nepalese pilgrim. Journal of Applied Physiology 18, 1234-1238

Forest Buffalo in the Republic of Congo. What Species Is That?

Forest Buffalo
Kurt Dundy at English Wikipedia

As a detached but interested outsider looking in on the world of taxonomy and systematics, I have been kept entertained by the arguments and battles between parties and concepts that have raged over the decades. When looking over Lango Bai in the Republic of Congo in May, all these arguments coalesced into one thought: what species are these, referring of course to the Forest Elephant and the Forest Buffalo? I considered the Forest Elephant in my earlier post (16 June with video showing these two species). More recently, I have been looking up what the current thoughts are on the status of Forest Buffalo, a very different looking animal from its savanna counterpart.

From our all too brief observations in the Congo, the name Forest Buffalo seems inappropriate. They were all in the patches of savanna that characterise this region or in the bai. Indeed, work in the Central African Republic on their local distribution found them to be ‘highly dependent on clearings, as well as on the more open forest stands, characterised by large trees and open canopy’.

I always start to twitch when I read that the Forest Buffalo is a subspecies of Syncerus caffer. I hate the use of subspecies as a concept and regard it as an example of the past muddleheadedness of people who cannot bear uncertainty. However, that is not to say that geographical variation is not important nor that conservation measures based on geographical populations are not worthwhile.

The standard treatment of African buffalo is to treat the Forest form as a subspecies of S. caffer, S.c. nanus. In early years, the mammalian morphologists had it split as a separate species whereas mammalian taxonomists of the last century tended to be lumpers. Across Africa, the view was taken that these populations were freely inbreeding and, therefore, the same species.

The late Peter Grubb and his co-author Colin Groves took a different approach. They adopted the phylogenetic species concept to examine African ungulates. This species concept can be summed up informally as: if it looks markedly different then it is different. Applying this species concept and using quantitative morphometric data, they found a clear grounds for separating Syncerus nanus, now a full species, from Syncerus caffer. Such revisions brought howls of protest from some quarters on the grounds that conservation measures would be more difficult to apply with so many more species split on similar grounds. That argument, to me, is worthless: conservation policies must be informed by the science however uncomfortable that may be for practitioners and fundraisers of the former; scientific hypotheses guided by conservation politics are not science at all. They published their results in a book, Ungulate Taxonomy, published in 2011, nearly five years after Peter Grubb’s death.

I greatly enjoyed reading Groves and Grubb’s chapter, Theory of Ungulate Taxonomy since it neatly speared many of the trendy pursuits such as gathering DNA data, explained simply the problems in applying the biological species concept and discussed whether phenotypic plasticity can explain morphometric differences. In their criticism of using only mitochondrial DNA to provide “molecular evidence” they relate the story of sika and wapiti deer. I had not heard it and so I repeat it here:

The third reason is, of course, introgression. Hybridization between two species is frequently asymmetrical. This idea was put forth more than half a century ago by Flerov, who described hybrids between sika and wapiti in N China and the Russian Far East: “These hybrids are encountered comparatively frequently in the wild state and have been long known to the Chinese. The male wapiti during rutting drives away the weaker spotted deer male and covers his females. If this superiority of wapiti stags also applied in F1 and subsequent generations—as it well might since the size of the hinds would increase in consecutive backcross generations, and they would become accessible only to wapiti stags—then the proportion of sika DNA would halve in each successive generation, until we would end up with populations that were effectively wapiti but with sika mtDNA. This effect, known as nuclear swamping, seems widespread along ruminants…”.

So what is the available “molecular evidence” on the Forest Buffalo? Well there is some but as far as I can see it is all on mtDNA. I have read it but until nDNA results are reported I shall not consider it further here.

My guess at the moment is that Groves and Grubb are right and that it will be shown that the Forest Buffalo, S. nanus, is a ‘good’ species with a hybrid zone around it.

However, the physiologist then takes over. How many genes are responsible for the morphological differences between the two species and how—and when—do the products of those genes exert their effects?

Groves C, Grubb P. 2011. Ungulate Taxonomy. Baltimore: Johns Hopkins University Press.

Melletti M, Penteriani V, Boitani L. 2007. Habitat preferences of the secretive forest buffalo (Syncerus caffer nanus) in Central Africa. Journal of Zoology 271 178-186.

In Search of a Penguin’s Egg. Why?...What happened to Nelson Norman's 1959 embryos?

Following on from my earlier posts of 8 April and 26 June, I have to make it clear that this is an interim account of what I have been able to find on this story as it extends into the 1950s and 60s. This is because I do not have ready access to some of the reports which are in libraries a long way away from where I live. However, I can certainly lay down the bones of the story and then follow up with more detail, if the original sources do not confirm the second-hand accounts, when I am next in London.

If you have read my first post on this topic you will see that my curiosity was aroused by reading Nelson Norman’s 2009 book, In Search of a Penguin’s Egg. Nelson Norman makes it clear that he was not only miffed by the reception he received on taking the Emperor Penguin embryos gathered with great difficulty and not a little danger during the antarctic winter of 1959 to Professor Glenister at Charing Cross Hospital but also by the fact that he had not been able to find out what happened to them:

I enquired several times over the years and was persistently told by FIDS that the embryos were being worked on…Nearly fifteen years later when I was in a position to consider the matter further and was a research director myself I went to the British Antarctic Survey (as FIDS was known by that time), expressed my concern, and asked for my embryos back saying that I would find an interested embryologist and we would work them up between us. This was agreed but when it asked for the embryos, the Survey was told that a technician had accidentally disposed of them!

It is now evident from the literature that the embryos were worked on and a report written. However we need to take a step backwards in order to take the story forwards.

Bernard Stonehouse collected a series of Emperor Penguin embryos in 1949; these Glenister examined. A short account of his findings is Nature in 1953. He also wrote a report for FIDS which was published in 1954. I have not yet seen the latter. His letter to Nature contains little of real substance (not unusual for Nature in those days). He wrote:

…comparison of the development of the external form of the Emperor penguin with that of the chick and with that of other penguins already described, namely, Gentoo and Ring penguins by Parsons and Gentoo and Adelie penguins (Pygoscelis adelia [sic]) by Waterston and Geddes, reveals a fact not yet recorded and worthy of note. In the earlier embryos the head region is relatively smaller, the neck and tail regions relatively longer, and the curvatures less well marked in penguin than in chick embryos. These features are more marked in Emperor penguin embryos and result in early penguin embryos resembling early reptilian embryos more closely than do chick embryos.

To which, I am afraid, my response is a very loud So What?

In his full report for FIDS (which I repeat I have not seen), C.Herbert, in his 1967 report on embryonic development in the Adélie, states:

More recently, Glenister (1954) investigated a series of 16 embryos of A. forsteri. Nine of the youngest were sectioned serially and a number of features which he considered primitive were listed. Glenister concluded that penguins are the most primitive birds, and that A.forsteri is the most primitive penguin.

How Glenister came to the conclusion that penguins are the most primitive birds I do not know.

That embryology could provide the answer was still being peddled in the 1960s. For example, the Committee on Polar Research of the National Academy of Sciences of the USA produced a report in 1961 stating:

Wilson and others made an extremely hazardous winter journey to collect emperor penguin embryos, hoping they would show reptilian features (Cherry-Garrard 1922), but the features were not found (Parsons 1934). Glenister (1954) describes eight features of the emperor embryo which suggest that penguins are primitive birds, and the emperor the most primitive of all…A study of a series of Antarctic penguin embryos of known ages is still awaited.

In view of Nelson Norman’s experience, I was surprised to find Herbert’s report of his work on the Adélie contains the information on what happened to the Emperor embryos Norman had collected:

The most recent description of embryos of the emperor penguin was by O’Gorman (1964) on embryos collected during the Royal Society International Geophysical Year Antarctic Expedition, 1955-59. He used the unpublished notes of J. [Nelson] Norman to calculate the ages of these embryos. Norman’s timed series of embryos, although in poor condition and small in number, enabled O’Gorman to adopt a multiplication factor of 2.9 to calculate the ages of the penguin embryos from the equivalent chick stages described by Hamburger and Hamilton (1951).
Both Glenister and O’Gorman expressed the need for an accurately timed series of developmental stages of a representative penguin. To fulfil this need a timed series of embryonic stages of P. adeliae, P. antarctica and P. papua was collected at Signy Island, South Orkney Islands, during the period January 1965 to February 1966.

So Nelson Norman had been incorrectly informed when he made his enquiries. Not only had his embryos been used but a report had been written and published in 1964.

I then found that Fergus O’Gorman had also been in the Antarctic at the same time as Norman as a zoologist with FIDS/British Antarctic Survey from 1957 to 1960 (working with my old dining companion, the late Nigel Bonner, in 1958). Half of O’Gorman’s entry can be seen in the online Google extract from the 2001 (3rd) edition of The Environment Encyclopedia and Directory and shows that he was a researcher at Charing Cross Hospital Medical School between 1960 and 1962; in other words he was working with Glenister on the embryos collected by Norman during this time.

Why nobody told Norman what had happened to his embryos seems an extraordinary oversight.

But the idea that the penguin embryo was going to reveal the origin of birds lingered on. The September 1968 issue of Antarctic, a news bulletin published by the New Zealand Antarctic Society, contained the following (my underlining):

American Programme for 1968-69

On June 28 the following ambitious 1968-69 United States Antarctic Research Programme was announced by the National Science Foundation in Washington

Iowa State University — Early Embryology of the Adelie Penguin
Dr. J. R. Baker and a field assistant from the Iowa State University, Ames, will continue the study of the early stages of the Adelie penguin embryology. The research will again be conducted at Hallett Station and Dr. Baker will seek to determine the effect of climate on incubation and how the Adelie embryo is formed. It is hoped that these studies may provide information on the evolutionary origin of penguins, whether from flying birds or reptiles. Following the Antarctic field work additional work will be carried out at the Iowa State University laboratories.

John R.Baker (1930-2012) did not publish on the evolutionary origin of penguins, whether from flying birds or reptiles. He did, however, follow up earlier observations that the rate of embryonic development is slow in penguins compared to other birds and that incubation period and the temperature of eggs in the nest vary in this species. In other words, he turned embryology into a study in physiological ecology to determine the effects of incubating Adélie penguin eggs at different temperatures.

I find it remarkable that the Edward Wilson’s big ‘thing’—getting embryos of the Emperor Penguin—was still being quoted as the justification for research on penguin embryos nearly 70 years after the discovery of the Cape Crozier rookery. Haekel’s recapitulation theory was dead in the water; all the evidence pointed to flying birds being the ancestors of penguins, and yet the idea, by now it seems a meme, ran on and on in the Antarctic exploration community.

Nelson Norman’s book led me to read the classics from the period of Antarctic exploration, including the superb Apsley Cherry-Garrard’s, The Worst Journey in the World. That led me off in other directions…but I cannot end this series without showing Edward Wilson's Sunset on Mount Erebus.

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Baker J R. 1969. Studies of the rate of development of the Adélie Penguin embryo. Antarctic Journal 4, 116

Committee on Polar Research of the National Academy of Sciences-National Research Council (1961). Science in Antarctica. Part 1. The Life Sciences in Antarctica.

Glenister, T W. 1953. Embryology of the emperor penguin (Aptenodytes forsteri). Nature 171, 357.

Glenister, T W. 1954. The Emperor penguin Aptenodytes forsteri Gray: II. Embryology. Falkland Islands Dependency Survey Scientific Reports No. 10. London: HMSO

Herbert C. 1967. British Antarctic Bulletin 14, 45-67

O’Gorman F. 1964. Observations on emperor penguin embryos. In The Royal Society International Geophysical Year Antarctic Expedition, Halley Bay, Coats Land, Falkland Islands Dependencies, 1955-59. IV. Meteorology, glaciology, appendixes. pp 353-363. Ed Blunt D. London: Royal Society.

Weinrich J A, Baker J R 1978. Adélie Penguin (Pygoscelis adeliae) embryonic development at different temperatures. Auk 95, 569-576

In Search of a Penguin’s Egg. Why?...Continued

Since writing In Search of a Penguin’s Egg. Why? on 8 April, I have read more and more on antarctic exploration in order: first, to understand why Edward Wilson, chief of the scientific staff of Scott’s final (1910-1912) expedition and who died with Scott, was willing to go to such lengths to obtain embryos of the Emperor Penguin; second, to try to understand why the Falkland Islands Dependency Survey (FIDS) was still trying to collect embryos in the late 1950s. I have also found, in the literature, the fate of the embryos collected by Nelson Norman in 1959.

However, the Scott expeditions (Discovery, 1901-04; Terra Nova, 1910-1912) were not the first to collect penguin embryos. Robert Neal Rudmose Brown (1879-1957) and James Hunter Harvey Pirie (1878-1965), members of the Scottish National Antarctic Expedition led by William Speirs Bruce (1867-1924), collected embryos at different stages of development of the Gentoo (Pygoscelis papua) and Adélie (P. adeliae) penguins. These embryos were brought back to Edinburgh where they were examined by David Waterston and Auckland Campbell Geddes of the anatomy department ‘through the kindness of Dr W.S. Bruce’.

The Scottish National Antarctic Expedition^‡ left Troon on 2 November 1902. Scotia, formerly the Norewegian whaler Hekla, had been refitted for the antarctic at the now defunct Ailsa shipyard in Troon, a short distance from where I shall be teeing off from the 1st at Royal Troon at 7.50, as usual on Fridays, tomorrow morning (weather permitting, of course). This successful expedition returned on 21 July 1904 to the Marine Biological Station at Millport, now sadly reduced to a study centre for schools. I shall return to the Scottish National Antarctic Expedition later since its very existence has a bearing on later developments.

Route of the Scotia

Scotia

Waterston and Geddes wrote up their findings for the expedition’s report published on 21 October 1909.

With regard to these developmental facts the question arises:— Is the duck's or the penguin's wing the more direct descendant of the common ancestor; or have they both diverged from the common stock approximately equally, but in opposite directions. Embryology alone cannot answer this question, but the evidence is clear in this, that the fore limb of the penguin in its development goes through a progressive and continuous series of stages along one unbroken line. The mesoblastic portion of the fore limb elongates, but its characters do not alter. It elongates, however, with a relatively greater rapidity towards the end of development, whereas the duck's fore limb, after being relatively longer than the penguin's ever is, regresses rapidly. So that the answer to our question, so far as the embryological evidence is concerned, must be that the wings of both these birds are different from the ancestral wing, and that the differentiation has been in opposite directions and that the common ancestor was a flying bird of a somewhat primitive type depending in large measure for the spread of its wing upon bone and muscle.

Their conclusions could not be more clear; the ancestor of modern birds and penguins was a flying bird.

One of the two laboratories on Scotia

Bruce had placed his penguin specimens with two of the leading anatomists/embryologists in Britain. David Waterston was demonstrator in anatomy at Edinburgh. In 1909, the year of publication of the report, he went to the chair at King’s College, London but in 1914 moved to the Bute chair of anatomy at St Andrews (as a golfer he perhaps could not resist the temptation of the Old Course). He died at the age of 70 in 1942, still occupying the Bute chair.

Coats Land. The expedition named this part of the
continent for the Coats family, the sewing cotton
manufacturers (now the multinational Coats plc),
who funded the expedition.

Auckland Campbell Geddes went on to a remarkable career. At the time of the penguin work he was assistant to the Professor (only one per department in those days), D.J. Cunningham, author of the famous Manual of Practical Anatomy. On graduation in 1908, he was appointed demonstrator. He was late to qualify because he had interrupted his medical studies to serve in the Highland Light Infantry during the Boer War.

His first public achievement from 1908 lived on until recently. His suggestion that the army volunteer force should be named The Territorial Force was adopted by Lord Haldane (JBS’s uncle), then Secretary of State for War. In 1909 he went to Dublin as Professor of Anatomy and then, in 1913, to McGill University in Montreal. He returned on the outbreak of war. He rose from Major in the 17th Northumberland Fusiliers in 1914 to Brigadier-General and Director of Recruiting at the War Office in 1916-17. He was then elected Member of Parliament for Basingstoke and Andover in 1917, becoming Minister of National Service from 1917 to 1919. He was then British Ambassador to Washington from 1920 to 1923. Sadly, he lost the sight of one eye. After his recovery, he served as Chairman of Rio Tinto. in 1942 he was injured by a flying bomb and also lost the sight of his other eye. He became Baron Geddes of Rolvenden in 1942. He died in 1954, aged 74.

The collectors of the penguin eggs also became well established. Rudmose Brown (1879-1957) was botanist on the Scotia Expedition. After working for Bruce after their return, he turned to geography, becoming Lecturer at Sheffield in 1907 and Reader at Manchester in 1920. He returned to Sheffield as Professor of Geography in 1931, retiring in 1945. In both World Wars, he served in Admiralty intelligence. Throughout, he continued his interest in the Arctic and Antarctic. He died in Sheffield in 1957.

Pirie (1878-1965) was the expedition’s medical officer, geologist and bacteriologist. On his return he was a medical practitioner in Edinburgh until 1913 when he joined the Colonial Service as a bacteriologist in Kenya. He was Deputy Director of the South African Institute for Medical Research from 1926 until 1941. In 1940 he gave the name Listeria (after Joseph Lister) to the bacterial genus. In 1948 he was living in Bournemouth on the south coast of England.

So, did Wilson not realise that the findings from the Scotia expedition would render his quest for Emperor penguin embryos unnecessary? Or did he judge the Emperor to be so different, in fact unrelated to the Adelie and Gentoo, that he thought the findings irrelevant? Was he even aware of the results from the Scotia expedition? Was he too busy with his work on the grouse disease inqjuiry and preparing for the Terra Nova expedition to study Waterston and Geddes’s findings between their publication in October 1909 and the departure of the Terra Nova in June 1910? I have been unable to find the answers to any of these questions from reading about Edward Wilson.

However, here’s where the politics of polar exploration kicks in. The Scotia expedition and its leader, Bruce, were regarded as the lowest forms of life by the power broker in British antarctic exploration, Sir Clement Markham, President of the Royal Geographical Society. All my reading indicates that Markham was rightly considered by later commentators a classic Monster. However, Markham’s personality is beside the point. The animus to Bruce was so great that I find it difficult to see Wilson raising any of the (excellent) results of that expedition in discussions over whether it was worthwhile to attempt the journey to Cape Crozier to collect the Emperor embryos with Markham in full control of the expedition and Scott, Wilson’s friend but Markham’s protégé.

From what I have read so far, I conclude that the collection of Emperor embryos was Wilson’s big ‘thing’ and had been his big ‘thing’ since his earlier discoveries on this species in the Discovery expedition of 1901-1904.

Geoge Seaver, in his book on Wilson, states that he gave three lectures to fellow expedition members and that ‘his own notes of them have been preserved but those taken by Scott and others are not without interest…In his second lecture he traced the descent of Penguins from the primitive lizard-bird, explaining their anatomy, and finding corroborative evidence in their primitive fossilized remains’. Those notes could well be worth examining anew to see what Wilson’s understanding was at that time.

Apsley Cherry-Garrard, Wilson’s protégé, who with Wilson and Bowers undertook that indescribable winter journey from Cape Evans to the rookery at Cape Crozier wrote in The Worst Journey in the World:

What is this venture? Why is the embryo of the Emperor penguin so important to Science? And why should three sane and common-sense explorers be sledging away on a winter's night to a Cape which has only been visited before in daylight, and then with very great difficulty?The Emperor is a bird which cannot fly, lives on fish and never steps on land even to breed. It lays its eggs on the bare ice during the winter and carries out the whole process of incubation on the sea-ice, resting the egg upon its feet, pressed closely to the lower abdomen. But it is because the Emperor is probably the most primitive bird in existence that the working out of his embryology is so important. The embryo shows remains of the development of an animal in former ages and former states; it recapitulates its former lives. The embryo of an Emperor may prove the missing link between birds and the reptiles from which birds have sprung*.

After the deaths of Scott, Wilson, Bowers, Oates and Edgar Evans on their return from the Pole, Cherry-Garrard obtained a series of embryos from Adélie Penguins at Cape Royde. He wrote:

It was always Wilson's idea that embryology was the next job of a vertebral zoologist down south. I have already explained that the penguin is an interesting link in the evolutionary chain, and the object of getting this embryo is to find out where the penguins come in. Whether or no they are more primitive than other nonflying birds, such as the apteryx, the ostrich, the rhea and the moa, which last is only just extinct, is an open question. But wingless birds are still hanging on to the promontories of the southern continents, where there is less rivalry than in the highly populated land areas of the north. It may be that penguins are descended from ancestors who lived in the northern hemisphere in a winged condition (even now you may sometimes see them try to fly), and that they have been driven towards the south. 

If penguins are primitive, it is rational to infer that the most primitive penguin is farthest south. These are the two Antarcticists, the Emperor and the Adélie. The latter appears to be the more numerous and successful of the two, and for this reason we are inclined to search among the Emperors as being among the most primitive penguins, if not the most primitive of birds now living: hence the Winter Journey. I was glad to get, in addition, this series of Adélie penguins' embryos, feeling somewhat like a giant who had wandered on to the wrong planet, and who was distinctly in the way of its true inhabitants.

So Cherry-Garrard in 1922 seems to be expressing a different reason for collecting embryos—that the most southern could be the most primitive penguins but not the most primitive bird—from Wilson in 1910. But the phrase if not the most primitive of birds now living could be taken to mean that it still might be shown that the Emperor is the most primitive bird. Alternatively, if not actually means even if not.  I tend to think it means the latter since otherwise he would be contradicting himself in these paragraphs.

Cherry-Garrard collected embryos from the Adélies during that period after the remaining members of the expedition found the bodies of the polar party, Scott, Wilson and Bowers. Surely Wilson in the many months they had together would have mentioned to Cherry-Gerrard whether Adéle embryos had been examined previously. That leads me to think that Wilson had not seen the report of the Scotia Expedition before embarking on Terra Nova. Original documents and notes on the contents of the libary taken by Scott and his party could well provide more information.

The story of penguin embryos does not end there…

----------------------

Waterston D, Geddes AC (1909) Report upon the anatomy and embryology of the penguins collected by the Scottish National Antarctic Expedition. Transactions of the Royal Society of Edinburgh 47 part 2, number 10, 223-244

Seaver, G (1933) Edward Wilson of the Antarctic. Naturalist and Friend. London: John Murray

*There is a difference in wording between the Pimlico edition 2003 (Vintage 2010) and that available online as a Project Gutenberg eBook; the latter appears to be from the original 1922 edition published by Constable in 1922.

‡Excellent photographs of the expedition are at:

http://gdl.cdlr.strath.ac.uk/scotia/  and  http://special.lib.gla.ac.uk/exhibns/month/apr2004.html

Forest Elephants in the Republic of Congo. What Species Were We Observing?

Opportunities to see the animals of the central African rainforests do not come every day. So the privilege of being able to visit groups of lowland gorillas and observe the other mammals, birds, reptiles and amphibians in the Congo Basin is an experience of a lifetime. In the middle of May we were with a group of ten clients of Naturetrek in the camps in the Republic of Congo run by Wilderness Safaris, Ngaga and Lango, 340 miles from Brazzaville, both in or adjacent to the Odzala-Kokoua National Park.

Lango Camp (the word ‘camp’ should be in inverted commas) is situated with views from the raised deck of Lango bai. Watching the bai as animals turn up is a delight, especially in the early morning when large flocks of African Green Pigeons fly overhead and African Grey Parrots appear from the forest to eat mud churned up by the elephants and buffalo. And by elephants I mean Forest Elephants and by buffalo, Forest Buffalo. Later in the day, solitary Bushbuck appeared and, just after our arrival, a Sitatunga.

This video shows what we saw at Lango Camp.

Talking about Forest Elephants with our guides, Justine, Alon and Adam, and the differences between forest and savanna elephants I knew that over the last century there had been arguments to and fro as to whether the Forest Elephant was a different species from the African Elephant. All the more recent books seemed to repeat the view that there was only one species of Elephant in Africa. I was also vaguely aware that the Forest Buffalo was not considered to be a separate species and that, recently, the Bushbuck had been split by somebody into two species.

Because when I actually saw Forest Elephants for the first time in the flesh and could appreciate that morphologically they were very different from the elephants we had seen in other parts of Africa, I resolved to look up their status in more detail when we got back.

Behaviourally too the Forest Elephant is very different. The nocturnal shrieks and cries that kept us awake as elephants gathered further down the bai were very different from the silence or low grumblings of other elephants. My natural tendency as a ‘lumper’ to think of one species of elephant in Africa was being shaken to the core at 2.00 am.

To cut a long story short, I am now convinced by the evidence available that the Forest Elephant is a separate species, that named by Matschie in 1900 as Loxodonta cyclotis. But in reading the papers, I was struck by the strange reluctance of many to accept this conclusion. IUCN still lumps all the elephants in Africa as Loxodonta africana.

Leaving aside the morphological differences and questions of gene flow between Forest and Savanna or Bush Elephants for the moment, the arguments that have arisen in the past 15 years or so have centred on genetic differences in populations of elephants in Africa. Different results were obtained using mitochondrial DNA (mtDNA) compared to nuclear DNA (nDNA).

The use of nuclear DNA to determine the phylogeny of elephants has been championed by Alfred L Roca’s group at the University of Illinois at Urbana-Champaign. Their first work was published in 2001 and showed a clear distinction between Forest and Savanna elephants. However, the single-species-in-Africa view continued as more work using mitochondrial DNA showed a number of geographically based clades. Nevertheless, continuing work by Roca’s group on nuclear DNA demonstrated that Forest and Savanna elephants were different and that mitochondrial DNA does not provide information on which the phylogeny of these species can be determined. In short, mitochondrial DNA provides a historical record of only the maternal line and with the introgression of genes by early hybridisation between separating lines during speciation or by later hybridisation leading to some fertile offspring, the mitochondrial DNA may bear no relation to the nuclear DNA of the species as a whole. As one paper (Rohland, Reich, Mallick, Meyer, Green, Georgiadis, Roca & Hofreiter, 2010) puts it:

…mtDNA represents just a single locus in the genome and need not represent the true species phylogeny since a single gene tree can differ from the consensus species tree of the taxa in question. Generalizing about species relationships based on mtDNA alone is especially problematic for the Elephantidae because their core social groups (‘‘herds’’) are matrilocal, with females rarely, if ever, dispersing across groups. This results in mtDNA genealogies in both African and Asian elephants that exhibit deeper divergence and/or different phylogeographic patterns than the nuclear genome.

Further strengthening of the case for two species in Africa came from work comparing these two elephants with the Asian Elephant and the relatively recently extinct Woolly Mammoth and American Mastodon.  Rohland et al. (2010) reported (with my emphasis in bold characters):

We have used a combination of modern DNA sequencing and targeted PCR amplification to obtain a large data set for comparing American mastodon, woolly mammoth, Asian elephant, African savanna elephant, and African forest elephant. We unequivocally establish that the Asian elephant is the sister species to the woolly mammoth. A surprising finding from our study is that the divergence of African savanna and forest elephants—which some have argued to be two populations of the same species—is about as ancient as the divergence of Asian elephants and mammoths. Given their ancient divergence, we conclude that African savanna and forest elephants should be classified as two distinct species.

And then, on the two African species (with references deleted):

Our study also infers a strikingly deep population divergence time between forest and savanna elephant, supporting morphological and genetic studies that have classified forest and savanna elephants as distinct species. The finding of deep nuclear divergence is important in light of findings from mtDNA, which indicate that the F-haplogroup is shared between some forest and savanna elephants, implying a common maternal ancestor within the last half million years. The incongruent patterns between the nuclear genome and mtDNA (‘‘cytonuclear dissociation’’) have been hypothesized to be related to the matrilocal behavior of elephantids, whereby males disperse from core social groups (‘‘herds’’) but females do not. If forest elephant female herds experienced repeated waves of migration from dominant savanna bulls, displacing more and more of the nuclear gene pool in each wave, this could explain why today there are some savanna herds that have mtDNA that is characteristic of forest elephants but little or no trace of forest DNA in the nuclear genome. In the future, it may be possible to distinguish between models of a single ancient population split between forest and savanna elephants, or an even older split with longer drawn out gene flow, by applying methods like Isolation and Migration (IM) models to data sets including more individuals.

The problems inherent in using mitochondrial DNA have been stressed recently by Jerry Coyne in his blog, Why Evolution is True, in relation to the evolution of the Brown Bear and the Polar Bear in which conclusions drawn from mitochondrial DNA have been shown to confuse rather than illuminate. This is a screen grab from his blog:

This entry can be found at:
http://bit.ly/1lJEwmH

IUCN still persists in lumping all the elephants in Africa into one species. However, in a hard-hitting paragraph in the discussion of their paper, Ishida, Oleksyk, Georgiadis, David, Zhao, Stephens, Kolokotronis & Roca (2011) state the case clearly and why it is important for practical conservation:

“Mitochondrial essentialism” and the conservation of Africa's elephantsGiven that mtDNA haplotypes among elephants are an unreliable indicator of overall genetic similarity it is unfortunate that mtDNA alone continues to be used as a guide to elephant genealogical affinities. This “mitochondrial essentialism,” the continuing use of mtDNA to partition populations and species, among elephants where morphological and nuclear markers have established that mtDNA patterns may be inaccurate or misleading, might lead to adverse results for elephant conservation, as the following examples illustrate: If mtDNA data were used as the sole basis for elephant taxonomy and population structure, elephants in the Guinean forest block could be recommended for translocation to the deserts of Mali, on the grounds that their mtDNA similarity implies that they must be genetically similar. Likewise, relying on mtDNA to infer population structure would mean that savanna elephants from Tanzania could be moved west into the Congolian tropical forest, since forest and savanna elephants in these regions share similar F clade mtDNAs. Either of these translocations would be inappropriate, since even while carrying mtDNA from the same haplogroup, individuals in forest and savanna locations are very different in nuclear genotypes, belong to different species, and are thus unlikely to thrive when moved to the wrong habitats. Although the examples are extreme, it may be equally troublesome that mtDNA-based misinterpretations of African elephant taxonomy constitute an unacknowledged potential hindrance to their proper conservation by convincing conservation groups to “continue to treat African elephants as a single species”.

Although studies based solely on mitochondrial DNA appear to be useless in this and many other cases, there is a bonus as Roca and his colleagues have both pointed out and actually worked on: the use of both nuclear and mitochondrial genetic markers can more accurately determine the geographical source of poached ivory.

But now we come full circle. The Forest Elephant was described as a new species by Professor Dr (Georg Friedrich) Paul Matschie (1861-1926) in 1900. Unfortunately, Matschie, who somehow rose to be Director of the Berlin Museum in 1924, was treated as a joke by fellow professionals. An anti-Darwinian mystic, he described a new species or subspecies from pretty well every specimen that fell under his gaze. Mammalian taxonomy seems to have suffered mightily as a result of his activities. His antics and those of his protégé are described, unfortunately briefly, by Colin Groves and the late Peter Grubb in their book, Ungulate Taxonomy (Johns Hopkins University Press, 2011). The ultimate splitter caused a lumping backlash. (Groves and Grubb, incidentally were responsible for the morphological work that resurrected the two-species-in-Africa idea in 2000.) I have the suspicion that Matchie’s involvement in erecting Loxodonta cyclotis may have been one of the reasons why there was such opposition to the possibility of the existence of a separate Forest Elephant in the last century. So, sadly, it appears that Matschie, for once, was right. Maybe right for the wrong reasons but right.

For those wanting more information, these papers and the references therein contain the story as it stands at the moment.

Roca AL,  Georgiadis N,  Pecon-Slattery J, O’Brien SJ (2001) Genetic Evidence for Two Species of Elephant in Africa. Science 293, 1473-1477

Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Koloktronis, S-O, Roca AL (2011) Reconciling Apparent Conflicts between Mitochondrial and Nuclear Phylogenies in African Elephants. PLoS ONE 6(6): e20642. doi:10.1371/journal.pone.0020642

Roca AL, Georgiadis N, O’Brien SJ (2004) Cytonuclear genomic dissociation in African elephant species. Nature Genetics 37 96-104

Ishida Y, Demeke Y, Van Coeverden de Groot PJ, Georgiadis NJ, Leggett KEA, Fox VE, Roca AL. Distinguishing Forest and Savanna African Elephants Using Short Nuclear DNA Sequences. Journal of Heredity 2011 610-616

Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M. (2010) Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biol 8(12): e1000564. doi:10.1371/journal.pbio.1000564

Sea Snakes: My Only Sighting

My earlier Post on the survival of  sea snakes at sea reminded me that I have only seen sea snakes in the wild once, and that was while gently walking from the restaurant at the Shangri La Tanjung Aru Resort, Kota Kinabalu in Sabah (North Borneo) in 1999. The snakes were crawling among the rocks below the concrete platform that forms the sea front. They were Laticauda colubrina, the banded sea snake. This site is mentioned in the Wikipedia article on this species as a place where they occasionally come ashore. According to that article, the males come ashore in the early evening and the females later.

Laticauda colubrina
Bernard DUPONT from FRANCE
Used on Wikipedia

Modified 9 November 2019