Wednesday, 23 July 2014

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








Tuesday, 22 July 2014

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
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

Saturday, 12 July 2014

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

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?

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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.

Thursday, 3 July 2014

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