KCite shortcode to insert a reference

One nice aspect is that the plugin formats a bibliography at the end of your blog post. I’ve had no problems with the plugin at all. Of course it is early days and it isn’t a fully-featured reference manager like desktop workhorses Zotero or Mendeley, but it is already very useful.

One slight problem I have is that several of my publications are in areas of biology not covered by PubMed, and I have two with broken doi numbers, one because it directs to somebody else’s paper (its fixed!) and one because Nature can’t spell and I refuse to link to a mangled website version of my paper.

What additions would I like? Not much really. I would like the ability to have reference summary popup on mouse-over the reference, that would be a useful thing for a web-based citation. Also perhaps more web-links from the reference section? I could name lots of other things but that wish list would be turning it into a fully-featured reference manager, which is unrealistic for a recent effort by academics rather than some large company. To be perfectly honest I’m surprised that there aren’t WordPress plugins already for Mendeley and Zotero.

The plugin was created by Biologists Phillip Lord, Simon Cockell, and Daniel Swan, who together run Knowledgeblog. The following quote describes their mission.

Welcome to Knowledge Blog. We are investigating a new, light-weight way of publishing scientific, academic and technical knowledge on the web.

The Problem

Scientific and academic publishing is a painful process for authors, reviewers and readers alike. No one really benefits from the current system which grew because of the expense of producing, printing and distributing books. The internet and the web technologies have changed this enormously, but still the uptake within scientific and academic publishing has been slow, and left much of the existing system in place; the reason for this is that some parts of the system are good: explicit authorship, peer-review and the ability to archive are the main ones.

We need a new solution, that removes the annoyances of the current system, while keeping the advantages.

The Solution

The solution is already available; we just need to use it in a different way. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.

Very interesting indeed, something I’m going to keep a close eye on. As for KCite, I can see it being regular addition to my posts.

References

1. S.P. Moss, D.A. Joyce, S. Humphries, K.J. Tindall, and D.H. Lunt, "Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage.", Genome biology and evolution, vol. 3, 2011.
2. D.H. Lunt, "Genetic tests of ancient asexuality in root knot nematodes reveal recent hybrid origins.", BMC evolutionary biology, vol. 8, 2008.

Cryptic Species: Illustration of genetically, geographically, ecologically and reproductively isolated 'groups' currently classified as the single bryozoan species Celleporella hyalina. From Gomez et al 2007

Rod Page at iPhylo draws attention to a new paper in Systematic Biology (Costello et al 2011) estimating the total number of species. They come to a much lower figure than a previous paper (Camilo Mora et al 2011). Rod said something interesting that linked in to my thoughts on species numbers.

“The fuss over the number of bacteria and archaea seems to me to be largely a misunderstanding of how taxonomic databases count taxa. Databases like Catalogue of Life record described species, and most bacteria aren’t formally described because they can’t be cultured. Hence there will always be a disparity between the extent of diversity revealed by phylogenetics and by classical taxonomy.”

These papers seem to be estimating the number of species that would be formally described if we carried on as we have been. The interesting thing is how this relates to the actual number of species that exist. I wonder what the slope of the line of increasing number of species formally described and the slope of informal ‘descriptions’ (eg from DNA) would look like? After all surely we are only really interested in the number of species in nature, not in our catalog of nature. Studies of the change in our estimates of a parameter are always less interesting and useful than the parameter itself, species number in this case.

Cryptic Species

Even putting consideration of bacteria and archaea aside, use of population level DNA barcoding has revealed large numbers of cryptic species. These are often, as you might expect, among small dull-looking taxa where its hard to tell them apart by eye (although we do also find cryptic species in very well characterised groups such as birds, and mammals).

My feeling is that it is very rare indeed for the outputs of DNA barcoding to lead to formal descriptions of species. This is partly because those scientists do not have suitable training and partly because species description is a very difficult and frustrating task.

Meiofaunal Community Sequencing

Meiofaunal community sequencing has suggested very large increases of biodiversity of eukaryotes compared to morphological approaches. Studies of nematodes for example reveals very large numbers of (conservatively judged) Operational Clustered Taxonomic Units (likely species or higher level groupings). The work of Si Creer and colleagues is particularly informative.

Remarkably, along only an 800 m transect, we detected 182 Nematoda OCTUs, compared with 450 species of Nematode that have been described from around the entire British Isles. From a geographical perspective, these data represent the discovery of 40% of the previously known phylum richness from a transect that represents 0.004% of the length of the British coastline (~17,820 km, Ordnance Survey). (Fonseca et al. 2010)

Yes we can argue about what is a species. Yes there can be problems with defining taxa by % sequence divergence alone. But really these would be fine-scale adjustments, its hard to get away from the fact that lots of lines of evidence suggest that there are a lot of undescribed species. Don’t forget that this isn’t DNA barcoding, this is species identification and discovery. Often when extensive geographic sampling is carried out on these small organisms they may additionally fall into cryptic species assemblies. So cryptic species complexes may be overlaid on top of this realisation that much/most biodiversity is undiscovered.

Will these species ever be described?

Will these species ever be described? No, they won’t. Almost none of these will ever be described formally, and yet they exist, they comprise a very important component of our ecosystems. This problem is not going to go away, and will likely get more evident with high throughput environmental sequencing. The approaches to estimating species numbers need to be more explicit (especially towards the press) about what they are actually counting. They are not counting species numbers, but the frequency with which people write up species descriptions, and I would argue that DNA barcoding and environmental sequencing remove any plausible correspondence between these two rates.

You could of course take the view that a species only exists when it has been formally described. I’m sure formal description is a good thing, but irrespective of their official status these species do exist, they do contribute to actual biodiversity, they do interact in networks, they do harm/help our soil, crops, livestock, and health. Unlike King Canute at some point we have to respond to the flood in a practical manner, and counting described species as if they were true estimates of species numbers is starting to look rather naive.

I don’t want to criticise these groups too much. I like anyone who has a go at species diversity estimation, and Camilo Mora et al in particular do look at links between described and actual species numbers, and it is always difficult to get the subtleties of your work over in the press. Its just that I am yet to really see this important difference come over in the reporting of this work, nor have I really seen many biologists (at coffee time, or the web) who see it. We are making the assumption that species description in birds and mammals represent ‘small beasties’, and that pre-molecular estimates are representative of post-molecular. Do you feel comfortable with those assumptions? I don’t really have new suggestions how we should estimate the true number of eukaryotic species on our planet, but we need to think much more broadly and critically about how we should estimate this. And don’t even get me started on the overlooked bacterial and achaean diversity…

References

Camilo Mora, Derek P. Tittensor, Sina Adl, Alastair G. B. Simpson, Boris Worm. How Many Species Are There on Earth and in the Ocean?. PLoS Biol 9(8): e1001127.doi:10.1371/journal.pbio.1001127

Mark J. Costello, Simon Wilson and Brett Houlding. Predicting total global species richness using rates of species description and estimates of taxonomic effort. Syst Biol (2011) doi:10.1093/sysbio/syr080

Gómez, A et al Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society B: Biological Sciences 274, no. 1607 (January 2007): 199. doi:10.1098/rspb.2006.3718

Fonseca, Vera G,  et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature communications 1 (January 2010): 98. doi:10.1038/ncomms1095

Creer, S et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology 19 Suppl 1 (March 2010): 4-20. doi:10.1111/j.1365-294X.2009.04473.x.

What makes it worse is that when this paper (the paper that got me a job) first came out early on the Nature website they had spelled my name wrong! Adjacent keys typo again. They fixed it eventually, but it took a while. When you are a postdoc applying for jobs it only adds to the stress.

So I decided to email them to let them know. After about 10 minutes looking for an appropriate way to contact them on the website I’ve just given up. Hey, I’ve got a job now, and it makes Nature look stupid not me.

Lunt, D. H., and B. C. Hyman (1997) Nature 387:247-247. PDF Animal mitochondrial DNA recombination (no doi in my citations anymore as it points to a webpage with a stupid unprofessional typo).

I can’t help agree but with Dienekes’ concern over the worrying power of unelected bodies to represent the community.

I am glad that the “Land and Sea Council” gave Willerslev its content. But, seriously, who are they to decide whether the hair sample should be used or not?

It could be argued that Haddon’s unknown hair donor did not authorize a particular use of his hair sample. But, it is ludicrous to expect people from the past to anticipate all the potential uses that their tissues may have in the future. Nor is there any evidence that the anonymous donor authorized some council representing 5,000 future Aboriginal Australians, including a few of his distant relatives to prevent it from being used.

I would take it even further though, in that even elected bodies such as governments do not have automatic rights to determine such ethical issues over their citizens. They are elected to collect taxes, fix roads and the like. If they do wish to set out ill-defined ‘ethical’ restrictions they should start putting them in their election manifesto immediately.

I do very little science that could be of ethical concern to anyone, yet ethics committees still manage to make my life worse. Their actions are often nonsensical, and occasionally even unethical. They often seem to be mostly constituted to protect organisations from criticism rather than to consider actual ethics. My university has ethical restrictions for all animals, not just those mandated by UK law (vertebrates). So, do we get rid of those fish parasites or not? One fish, lots of parasites, do we treat them equivalently? I love nematodes, but even I find equating them to be quite hard core ethics! I was once told that before I could run a student practical class I had to get a medical declaration from all students to their health status including infectious diseases and whether they were pregnant or not. I tried to point out that since I couldn’t use any of this information for any reason it seemed actually unethical to demand the students to tell me such personal information via these ethics forms. Appreciation of irony is not common among ethical committees.

Introns per bond

Something that is often overlooked when calculating the number of introns per nucleotide is that introns do not insert into nucleotides but rather the phosphodiester bonds between them. I would suggest therefore that the most accurate and effective way to specify density would be introns per bond. It seems reasonable that counting nucleotides is a convenient shorthand for this, but actually this shorthand leads to small but persistent errors. This is an unfortunate consequence of genome annotation restricting itself to nucleotides but genomic processes sometimes targeting bonds.

In the cartoon of a gene above CDS represents the protein coding region and UTR stands for the 5′ and 3′ untranslated regions. The dashes between nucleotides represent phosphodiester bonds joining the nucleotides. There are 6 nucleototides in the 5′-UTR, 9 nucleotides in the CDS and 5 nucleotides in the 3′-UTR. What would happen if we were to insert an intron in this sequence at the boundary of one of the gene regions? In which gene region would it be counted?

Coding regions almost always begin with a codon specifying a methionine residue- the start codon ATG. Nothing preceding this A nucleotide is counted as part of the CDS. Coding regions finish with a termination codon, TGA in the example above. This A nucleotide is the end of the CDS. By usual practice therefore any intron inserting into the bond between the T and the A at the 5′ end of the CDS would not be counted as part of the CDS, nor would any intron inserting into the bond between the A and the A at the 3′ end of the CDS. This is quite reasonable in many ways, but defining UTRs by reference to the CDS (after the last nucleotide, before the first nucleotide) means that the CDS has one less bond per nucleotide than do the UTRs! The 5′-UTR here has 6 nucleotides and 6 bonds, the 3′-UTR has 5 nucleotides and 5 bonds, but the CDS has 9 nucleotides and only 8 bonds where an inserting intron would be labelled as a ‘CDS intron’.

Does this matter?

Both yes and no. Counts using introns/nucleotide will be very similar to introns/bond. I am not claiming that work needs to be repeated or that substantial errors put into question previous work. But there are two issues here

1. We should do it right. Understanding the actual insertion process requires us to use the right language. We should label introns as inserting between nucleotides to avoid confusion. You may not be confused, but try writing a script that counts introns when everything is labelled by nucleotide position.
2. We can’t yet be sure what difference correct counts make in large data sets. The age of genomics is here. We can study hundreds of thousands of introns from lots of species and treat this mass of data statistically. The numbers of introns/nucleotide and introns/bond may look similar to our eyes, but trusting our savannah ape brains to make the right call is a risky strategy with big numbers.

Here are a few choice quotes about Bio-Linux

Bio-Linux 6 packs a wealth of bioinformatics tools, scientific software and documentation into a powerful and user-friendly 64-bit Ubuntu Linux system. Download Bio-Linux today and turn your PC into a powerful workstation in minutes.

Bio-Linux 6.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux 10.04 base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can also install Bio-Linux packages to handle new generation sequence data types.

FYI: I’m running OSX 10.6.8 (Snow Leopard) on a MacPro with 4GB RAM and 2x 2.8GHz Quad-Core Intel Xeon processors. The list below is going to take >1 hour.

Here’s what I did to install

1. Download and install VirtualBox from http://www.virtualbox.org/wiki/Downloads
2. Download Bio-Linux6 (2.2 GB) from http://nebc.nerc.ac.uk/tools/bio-linux/bl_download. Since this is a free, supported, software paid for by the UK taxpayer it would be really great for NBAF-W if you registered so that they can say ‘X people have downloaded this software’. Also please cite the paper (Field et al 2006) when you can.
3. Open VirtualBox and click “New” from the toolbar. Follow the installation Wizard.
4. Give your virtual machine a name like “BioLinux”, choose Linux as the operating system, and select Ubuntu 64 bit as the version.
5. Select the amount of RAM to give it- 1024MB should be OK, 512MB the default could be a bit mean. More RAM is always better, especially if you are going to set it to do a lot of hard work. This can always be changed later.
6. Virtual Hard Disk- use the defaults (create new), and again on the next screen (VDI).
7. Virtual disk storage details. “Dynamically allocated” is the default and I used this first time out. I suspect that it was the cause of slowness though and changed to “Fixed size” next time through. Certainly if you go for Dynamically allocated make sure to give it enough space on the following screen.
8. VD file location and size- I used 8GB and Dynamic first time through and it was immediately short of space after I did a system update. I would definitely choose 16GB if you have the space on your HD. When I compared the two this 16GB fixed size felt much faster.
9. The next screen is a summary and now you can press “Create” to create your virtual disk. If you have chosen “Fixed size” it will take a little while to create this virtual disk (5-10 mins) but will likely run faster in the future. At the end of the process you come back to exactly the same summary screen as at the start, with no indication that anything has happened. If you press the “Create” button again though it immediately updates to show you your new virtual disk in the VirtualBox Manager window.
10. You can now press the Green Start arrow in the toolbar to launch it. You will now get a “First Run Wizard”.
11. Select Installation Media. Now is the time to select the operating system that you specified in step 4, ie point it towards your download of BioLinux. If you click on the little folder icon to the right of the drop-down menu you can select your BioLinux file. Use the dropdown in the file list window to select “RAW (*.iso *.cdr)” as your BioLinux is an .iso file. Check your downloads folder to locate it. At this point it is very easy (I did it 4 times across 2 installs) to click on something that causes the screen to freeze and bleep whenever you click on anything. The Esc key solved this for me. Be careful where you click! When you have selected the file you should be back at the Select Installation Media dialog with bio-linux-6-latest.iso now selected. Continue.
12. The next screen claims that you are installing your file from CD/DVD, ignore that, you know the truth. Click Start.
13. You should now get an Ubuntu window and wait a couple of minutes before it boots and you see the BioLinux desktop and the install window.
14. Choose your language and “Install Bio-Linux 6″ at the bottom. Don’t click on “Try Bio-Linux”. Then select time zone.
15. Keyboard layout “Choose your own” then select “United Kingdom Macintosh” from the right panel.
16. Accept the defaults, then add your name and password. I set it to log in automatically here.
17. Now click INSTALL. Almost done. It will take a few minutes to install, go and have a coffee.
18. “Installation complete- you need to restart the computer.” This refers only to the virtual computer. Restart. “Please remove the disc and close the tray (if any) then press enter”. This is because the software still thinks you are installing from a DVD. Ignore it, and press enter, Ubuntu Bio-Linux will boot.

Notes

There is a nice piece about him on the IoZ website

• 2001-present: Senior Research Fellow and Head of Research Theme: Genetic variation, fitness and adaptability, Institute of Zoology, Zoological Society of London.
• 1995-2001: Research Fellow, Institute of Zoology, Zoological Society of London.
• 1994-1995: Research Fellow, Insect Molecular Genetics Group, Institute of Molecular Biology and Biotechnology, Heraklion, Crete.
• 1992-1994: Research Fellow, Department of Biology, University of Louisiana, Lafayette, Louisiana.
• 1991-1992: Research Fellow, Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, Queen’s University, Belfast.
• 1990-1991: Research Fellow, Department of Molecular and Cell Biology and Department of Zoology, University of Aberdeen.

I also thought I’d post some of his publications

Lopez-Vaamonde, C. et al. Lifetime reproductive success and longevity of queens in an annual social insect. JOURNAL OF EVOLUTIONARY BIOLOGY 22, 983-996 (2009).

Gardiner, A., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Sites of evolutionary divergence differ between olfactory and gustatory receptors of Drosophila. BIOLOGY LETTERS 5, 244-247 (2009).

Zaki, S.A.H., Jordan, W.C., Reichard, M., Przybylski, M. & Smith, C. A morphological and genetic analysis of the European bitterling species complex. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 95, 337-347 (2008).

Gardiner, A., Barker, D., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Drosophila chemoreceptor gene evolution: selection, specialization and genome size. MOLECULAR ECOLOGY 17, 1648-1657 (2008).

Paulo, O.S. et al. The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean. MOLECULAR ECOLOGY 17, 1535-1551 (2008).

Gardiner, A., Barker, D., Butlin, R.K., Jordan, W.C. & Ritchie, M.G. Evolution of a Complex Locus: Exon Gain, Loss and Divergence at the Gr39a Locus in Drosophila. PLOS ONE 3, (2008).

Ciborowski, K.L. et al. Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations. CONSERVATION GENETICS 8, 1355-1367 (2007).

Clark, A.G. et al. Evolution of genes and genomes on the Drosophila phylogeny. NATURE 450, 203-218 (2007).

Ciborowski, K.L. et al. Rare and fleeting: an example of interspecific recombination in animal mitochondrial DNA. BIOLOGY LETTERS 3, 554-557 (2007).

Garcia de Leaniz, C.G. et al. A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation. BIOLOGICAL REVIEWS 82, 173-211 (2007).

Lopez-Vaamonde, C. et al. Effect of the queen on worker reproduction and new queen production in the bumble bee Bombus terrestris. APIDOLOGIE 38, 171-180 (2007).

de Eyto, E. et al. Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 274, 861-869 (2007).

Dukes, J.P. et al. Isolation and characterisation of main olfactory and vomeronasal receptor gene families from the Atlantic salmon (Salmo salar). GENE 371, 257-267 (2006).

Sumner, S., Pereboom, J.J.M. & Jordan, W.C. Differential gene expression and phenotypic plasticity in behavioural castes of the primitively eusocial wasp, Polistes canadensis. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 273, 19-26 (2006).

Verspoor, E. et al. Population structure in the Atlantic salmon: insights from 40 years of research into genetic protein variation. JOURNAL OF FISH BIOLOGY 67, 3-54 (2005).

Jordan, W.C. et al. Allozyme variation in Atlantic salmon from the British Isles: associations with geography and the environment. JOURNAL OF FISH BIOLOGY 67, 146-168 (2005).

Pereboom, J.J.M., Jordan, W.C., Sumner, S., Hammond, R.L. & Bourke, A.F.G. Differential gene expression in queen-worker caste determination in bumble-bees. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272, 1145-1152 (2005).

Consuegra, S. et al. Rapid evolution of the MH class I locus results in different allelic compositions in recently diverged populations of Atlantic salmon. MOLECULAR BIOLOGY AND EVOLUTION 22, 1095-1106 (2005).

Consuegra, S., Megens, H.J., Leon, K., Stet, R.J.M. & Jordan, W.C. Patterns of variability at the major histocompatibility class II alpha locus in Atlantic salmon contrast with those at the class I locus. IMMUNOGENETICS 57, 16-24 (2005).

Lopez-Vaamonde, C., Koning, J.W., Jordan, W.C. & Bourke, A.F.G. A test of information use by reproductive bumblebee workers. ANIMAL BEHAVIOUR 68, 811-818 (2004).

Dukes, J.P., Deaville, R., Bruford, M.W., Youngson, A.F. & Jordan, W.C. Odorant receptor gene expression changes during the parr-smolt transformation in Atlantic salmon. MOLECULAR ECOLOGY 13, 2851-2857 (2004).

Lopez-Vaamonde, C., Koning, J.W., Brown, R.M., Jordan, W.C. & Bourke, A.F.G. Social parasitism by male-producing reproductive workers in a eusocial insect. NATURE 430, 557-560 (2004).

Lopez-Vaamonde, C., Koning, J.W., Jordan, W.C. & Bourke, A.F.G. No evidence that reproductive bumblebee workers reduce the production of new queens. ANIMAL BEHAVIOUR 66, 577-584 (2003).

Youngson, A.F. et al. Management of salmonid fisheries in the British Isles: towards a practical approach based on population genetics. FISHERIES RESEARCH 62, 193-209 (2003).

Paulo, O.S., Jordan, W.C., Bruford, M.W. & Nichols, R.A. Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard. MOLECULAR ECOLOGY 11, 809-819 (2002).

Paulo, O.S., Pinto, I., Bruford, M.W., Jordan, W.C. & Nichols, R.A. The double origin of Iberian peninsular chameleons. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 75, 1-7 (2002).

Paulo, O.S., Dias, C., Bruford, M.W., Jordan, W.C. & Nichols, R.A. The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 268, 1625-1630 (2001).

Youngson, A.F., Dosdat, A., Saroglia, M. & Jordan, W.C. Genetic interactions between marine finfish species in European aquaculture and wild conspecifics. JOURNAL OF APPLIED ICHTHYOLOGY 17, 153-162 (2001).

Jordan, W.C. & Bruford, M.W. New perspectives on mate choice and the MHC. HEREDITY 81, 127-133 (1998).

Jordan, W.C., Verspoor, E. & Youngson, A.F. The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon. JOURNAL OF FISH BIOLOGY 51, 546-560 (1997).

modern researchers are completely unaware of the history of their field. That’s partly because the work on bacteria and bacteriophage—where the basic concepts were often discovered—is no longer taught in biochemistry and molecular biology courses. This leads to the false idea, as expressed in the press release, that all new discoveries in eukaryotes are truly new concepts that nobody ever thought of before. The solution to this problem is to make all students read The Eighth Day of Creation.

I liked the quote from John Hawks too

I suppose we could rephrase Santayana: Those who ignore history feel privileged to reinvent it.

Judon wrote the truly epic book “The Eighth Day of Creation: Makers of the Revolution in Biology” which describes in detail the development of molecular biology from extensive interviews with its early pioneers. It’s a great read, his writing style is easy and absorbing, and the content fascinating. Despite not having yet finished the book, I can recommend it very highly indeed. What? Wait, you haven’t finished the book yet? How good can it really be? It’s a great book, but one that suffers from poor publishing by Cold Spring Harbor Press. Let me get my excuses out of the way now; I’m really busy, have little time for reading things that aren’t journal articles, and have a big backlog of other books to read. Yet these aren’t the real reasons. The real reasons are that it is enormous and only comes as a paper copy. The book, at 714 pages, is very weighty and thick even as a paperback. It is about as thick as a single volume of this size can be, and of course the pages themselves don’t open out very flat. It is pretty heavy and I have decided not to take it on holiday with me based on this alone. That is a shame, as holidays are when I catch up on reading.

There is a simple solution however – release it as an eBook. I would love to read this as a Kindle book on my iPad and be able to take it anywhere and just dip into it. It wouldn’t matter then how long it was. What is more I would be able to look stuff up when sitting in seminars and journal clubs, just quickly checking the history of a topic. Lastly I would like to be able to highlight and comment on sections. I have an absolute phobia of writing in books, I just can’t do it. Somehow (almost religiously) I know it is just plain wrong, even though I can’t think of a single reason why. I have no such qualms about marking up an eBook however, highlighting sections and adding notes. These notes and highlighted sections are searchable and easily found again- very useful indeed.

Although I really agree with Larry Moran’s concluding sentence “The solution to this problem is to make all students read The Eighth Day of Creation” I think that the chances are remote without good modern publishers helping the process along. Do something useful today, go to the Amazon webpage of Eighth Day of Creation and click on the link (usually just under the picture) to request a Kindle version from the publisher.

I’ve had a number of manuscript experiences where I’ve spent long hours trying to collate different authors’ contributions into the same Word document. The idea of using GDocs is that multiple authors can have the same document open at the same time making changes without any conflicts or the whole thing crashing. You never have to ask “which is the live copy?” since there is only one copy.

Good parts

• Nobody has had to collate mutually incompatible versions into one document and circulate (again) for people to check.
• It is a clean GUI and a pleasure to use.
• There is a good comment system and these are supplemented with a realtime discussion panel, just like Skype or other IM client.

Less good parts

• It doesn’t work well in some older browsers. Tell collaborators to use Chrome, otherwise they may complain that its a bit rubbish and doesn’t work properly. Using Chrome there are few to no problems (ie better than Word).
• You cannot use any sensible reference software. Mendeley, Zotero or any of the other reference managers you know will not allow you to insert references and format a bibliography the way you would in Word.
• Track changes is not as good as in Word.

Google Docs revision history

Overall its been great I think. There are a few things I really wish were different. Track changes could be easily improved to identify who has done what. Yes versions of the document can be compared, and rolled back to previous versions, both of which are useful but none of it is quite as obvious and easy to use as in Word. More than anything I really wish that reference management was better. We have been typing in place holders (Smith 2000) and then exporting the document as a Word file and introducing the citations using a reference manager before submission. This sounds bad. Why not just do everything in Word? Well, even today, two of us were making some last minute changes on the Word version, each copy with someone’s initials appended and somebody tomorrow has to reconcile it all.

I think Google Docs if adopted widely would have a great impact on writing multi-authored manuscripts. I don’t think it will be very widely used in science though unless reference managers can integrate with it properly. Despite this I have really enjoyed writing a manuscript with it, and, even though it has to be passed through MS Word at the end, on the whole I’ve much preferred it.

Although the desert living sticklebacks, and the dangerous rock pocket mice hunting snakes and owls come close, my personal favourite is the effect of public health measures on Indian morality.

“Alternative splicing is hybridising two different gentetic sets such as a snake and a monkey”

“introns are removed by using exons which occurs using protein synthesis”

“most of this work is done on mices”

“DNA is made up of proteins which are made up of amino acids. Each protein has a series of codons which are 3 amino acids that code for different things that each protein does in order to synthesis the DNA, such as Stop and Start codons.”

“Both species of chimpanzee are omnivores, having being observed feeding both on vegetation, such as shoots and leaves as well as animals, such as termites or small vertebrae.”

“Although there isn’t much difference between some of the A. fulgerator’s colour patterns or adult faeces, which would normally be assumed meant they were the same species”

“All the rest of the population may fall victim to the new virus, meaning extreme death of all the organisms… ”

“The saltwater sticklebacks have hard bony scales which help protect it from an attack by predators in the water such as sharks… ”

“The semi conservative and dispersive where then tested again with the use of testing the density gradient. 14N + 15N. This is used to see the effect of the weight of density”

“Rock pocket mice… It’s main prey are snakes and owls”

“The Pleistocene glacial cycles caused much of northern and central europe to be pushed south to refugia in Iberia, Italy and the Balkans.”

“The genetic change do not have polytechnic effect”

“SOX genes are intronless, which means they do not contain an intron”

“By 1903, just in India the plague was killing a million a year. However, the morality rate was overall much decreased in this plague due to the increased public health measures, and eventually, antibiotics.”

“Wild sticklebacks have had to adapt to thier surrounding. Their wild and dry surroundings….. to help them to conserve water and live through desert conditions”