Evo-Karma

Hacking the JPEG/PDF tree format

2011-10-26T21:27:00.000Z

Just back from giving a presentation at the Scottish Phylogenetic Discussion group in Edinburgh. Nice mix of talks. I think I got a lot of people thinking and talking about the way we are doing things and how we could improve the way we do things. The slides are available on Nature Precedings but it is a bit slow to load, so I have added it to slideshare as well.

Hacking the JPEG/PDF tree format

View more presentations from josephhughes.

The phyloscape changes quickly, we need to build a better way to keep track of it

2011-06-08T14:27:00.008Z

Since Hennig's 1969 major publication on the phylogeny of hexapod orders (Insecta + Entognatha), I have found more than 60 publications of phylogenies on the ordinal relationships within the group. Some may be re-analyses of the same data but it is still quite a large number of studies. Thirty-seven of these have been published in the last decade and this rapid change in the phylogenetic landscape of this group (and this is probably the case for many other lineages) is increasingly becoming hard to keep track of. Sure, you could do a regular Pubmed or WoS search for phylogen* + insecta but you then need to extract the phylogeny and put it in the context of previously published studies. Sure there are databases like TreeBase and PhyLoTa that provide ready-made phylogenetic reconstructions but the former has limited content and the latter has limited resolution at many nodes of interest.

It is important to have an up-to-date and complete image of the phylogenetic landscape of the groups we work on, even if the overall picture is blurry. This would provide a better idea of areas that require further taxonomic sampling and/or a larger number of characters to resolve the relationships of interest, it would also provide a valuable resource for comparative studies. For this to work, information needs to be integrated between different databases like PhyLoTA, TreeBASE, GenBank, Treefam etc. in an automated fashion as well as defrosting phylogenetic reconstructions from previously published studies (see my previous post). Perhaps a simple repository of third-party phylogenetic reconstructions would help: submitter - publication reference - figure number - phylogeny (newick, nexus, phyloxml, nexml ....). Although would anybody submit data? Perhaps I need to think of a way to reward those that do/

Reference

Hennig, W. 1969. Die Stammesgeschichte der Insekten. Frankfurt am Main, Germany: Kramer.

Recognition of tree images

2011-05-22T20:06:00.003Z

I have just published a program on the automated recognition of phylogenies from tree images. First of all, I would like to apologise for the use of the word 'towards' in the title, I know that it is increasingly being used and irritating to some. I just wanted to be honest in that this program does not succeed on all tree images but is a step in the right direction.

I thought I would take the opportunity to post a few links to software that deals with the same problem. We have all been rather unorginal with names!

TreeThief:

To my knowledge, this was the first program that dealt with the problem of converting a phylogenetic image back to the more useful bracket format such as NEXUS or newick. It requires the user to click on tips and nodes in a specific order and type in the label at the tips. Unfortunately, this program only works on MacOS 9.

TreeSnatcher:

TreeSnatcher was a conceptual advance on TreeThief, relies heavily on Java libraries and is cross-platform. It requires a limited amount of input from the user, such as selecting the foreground and background and lets the user improve the quality of the extraction thanks to this interactivity.

TreeSnatcher Plus:

TreeSnatcher Plus is an improvement on TreeSnatcher as it lets the user convert almost anything to a newick file, for example it works on radial tree images.

TreeRogue:

TreeRogue is essentially the same concept as TreeThief and I have just come across this so unfortunately do not make reference to it in my paper (sorry). It uses an R script that converts coordinates to a tree file. These coordinates can be detected from an image by using GraphClick, which costs $8.

TreeRipper:Image via Wikipedia

TreeRipper has been written in C++ and there is a version running on the website, the code is available under GNU GPL v3. It uses heavily the C++ API to to ImageMagick image-processing library (Magick++) and it uses Tessecract-ocr to convert the leaf labels to text. This is a fully automated approach that unfortunately only works on a proportion of the tree images. You could for example use TreeRipper for batch processing a large number of trees and then use a semi-automated approach for the trees that weren't converted.

There is still a lot of room for improvement and I am hoping that someone out there will make further progress on this interesting challenge.

Of course, none of these programs would be necessary if we all shared our trees and this would only be possible if we had a useful phylogenetic standard <= this statement should please the TDWG Interest Group on Phylogenetic Standards ;)

Reference:

Hughes, J. (2011). TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics 12: 178 doi: 10.1186/1471-2105-12-178

Insect systematics: you've got to laugh, if you didn't you'd cry

2011-05-20T14:05:00.005Z

In continuation from my previous post, I have now assembled 43 order level phylogenies of insects, i.e. they are based on more or less independent sources of data. The oldest study included is from 1993, so I still have my work cut out to find trees published before then especially as it becomes increasingly hard to get your hands on the articles as you go further back in time.
As more phylogenies are included, it also becomes hard to visualize this increasingly complex network on a 2D screen and I which I could explore it in a more intuitive way.

Many outstanding questions in the phylogenetic relationships of insect orders

2011-05-04T11:35:00.003Z

I am trying to get my head around the multiplicity of phylogenetic hypotheses for insect phylogenetic relationships in continuation from my previous post. I have been gathering a number of insect phylogenies from the literature (these include morphological and molecular based phylogenies). I wanted to illustrate where the hypotheses were conflicting so I used a SuperNetwork with no edge weights in SplitsTree. This gives an idea of how much conflicting evidence there still is at the base of the Pterygota and also the large number of studies that have focused on the Endopterygota, in particular the relationship of the Strepsiptera to the other orders. Many of the orders have only been included in one study, in particular the basal orders. What I would like to do at some point, is show how the insect phylogeny has changed over time by layering the phylogenies chronologically onto one another to form the above SuperNetwork.

Comparing the different hypotheses for Strepsiptera

2010-11-05T16:35:00.007Z

Image via Wikipedia
I have been comparing the different phylogenetic hypotheses for the Strepsiptera. As always, it has been hell to get the trees from images back into a suitable format for topology comparison. I have used the program METATREE for comparing multiple trees. The tree of trees essentially shows the two main hypotheses "Strepsiptera sister to Diptera" supported by the studies of Whiting and Wheeler using 18S and 28S rDNA, and at the other end of the metatree the "Strepsiptera sister to Coleoptera" supported by morphological studies and recent molecular studies using nuclear genes. Other differences in the Holometabola topologies are also illustrated in the metatree such as the variable position of the Hymenoptera. Anyway, to me, it looks like the research community is reaching a consensus on the "Strepsiptera problem": Strepsiptera sister to Coleoptera. What do you think?

TreeRipper: towards a fully automated optical tree recognition software

2010-10-15T19:59:00.004Z

Unfortunately my TreeRipper program has been rejected from BMC bioinformatics for now because there are too many delegate programs that the reviewers didn't manage to install successfully. So until I manage to find time to make a makefile that can deal with the installation on multiple platforms, I have put the manuscript on Nature precedings and you can find the code at google code. I think I am the first to attempt to fully automate the conversion of a tree image into something more useful for researchers and I hope that what I have done can be built upon and improved. I have attached to the code a set of images and tree files that might be useful for training and/or benchmarking future programs.

2nd UK RAD Sequencing Meeting: wrap-up #RADseq

2010-09-01T08:49:00.005Z

Image via WikipediaThe 2nd UK RAD sequencing meeting took place at the e-Science institute in Edinburgh. John Davey did a brilliant job of organizing the event and the e-Science is always a good venue for meetings and workshops.
The meeting was split into the morning session were we heard from the developers of RAD-sequencing and useful bioinformatic tools from John Davey: RADtools.
Dr William Cresko (Oregon) talked about the history of RAD tags and some recent applications in their lab which mainly center around understanding phenotypic evolution in the non-model three spined stickleback.
Dr Susan Bassham (Oregon) brought up quite a few practical issues on the molecular side of things. One that stuck to mind, is that it is much better to use restriction enzymes that will result in similar fragment sizes and smaller fragments are better so that the intensity of the dots on the Illumina cell are similar. Ideally, the GC content of your samples that you are planning to mix, should have similar GC-content, so mixing different species is probably not recommended.

Dr Paul Hohenlohe (Oregon) talked about cleaning up the data after sequencing. How to detect sampling biases: different tags, different alleles and sequencing errors. Other sources of error include PCR variance, polymorphisms at the RAD sites. All these need to be accounted for in the analyses. He has developed a maximum likelihood genotyping based on multinomial distribution of the reads. The sequencing error parameter is estimated independently for each site. His most recent paper goes into further detail.

Dr Simon Baxter (Cambridge) is using RAD-tags for gene discovery and linkage mapping in the Diamond-back moth. He is mainly interested in the evolution of resistance to pesticides.

Dr Maureen Liu (Nottingham) is using RAD-tag to determine the genetic mechanism for Left-Right chirality in the pond snail. Out of the 70,000 RAD-tags she got from cutting the 1.4Gb genome with the restriction enzyme SbfI, she found a subset of 19 that were linked to chirality. She also managed to link it to a specific gene but kept the name of the gene hush hush.

Dr Shapiro and Dr Justin Gerke (Princeton) used RAD-tag for a global survey of C. elegans. They found that some strains share nothing, others share everything but most share about 40% of their genome and 94% of the strain pairs analysed share one fragment. The fragments shared are also large. They suggest that this may be due to recent migration but selection, both background selection and positive sweep, may also play a role.

The remaining afternoon talks were about projects that were getting started and it was a good opportunity for the speakers to receive advice from the guys who had already used RAD-tag.

Developing RAD markers as a resource for plant breeding using the perennial ryegrass Lolium perenne. Dr Matt Hegarty (Aberystwyth)

Unearthing the functionally relevant genetic diversity from the earthworm
genome. Dr Pete Kille (Cardiff)
Exploring the use of RAD markers in tree breeding programmes. Dr Pablo Fuentes Utrilla (Edinburgh)
RAD Sequencing for applied conservation genetics. Dr Rob Ogden (TRACE Network, Edinburgh)
Adaptive signiﬁcance and genetic basis of a balanced colour-
polymorphism in Philaenus spumarius. Dr Octavio Paulo (Lisbon)
RAD genetic mapping of reproductive mode in tadpole shrimps. Tom Mathers (Hull)
The genetic architecture of a fundamental social trait. Dr Yannick Wurm (Lausanne)

All the talks were very honest about the difficulties of the approach. I really got the feeling that the community was working together to improve the technique and advise researchers on how to use the method.

Update: The talks are now available here.

Google Voice, Skype or TalkTalk

2010-08-26T10:51:00.007Z

Image via WikipediaThis morning, when I logged into my Google account, I got a little pop-up ad saying that I had $0.1 Google Voice credit. Prices seem cheap and I want to see whether it will be worth me using GoogleVoice instead of Skype for my calls. I have already posted a comparison of VoipCheap, Skype and Gizmo here. It looks like Google have set themselves up in direct competition with Skype so I am going to try to work out when I would be better off using GoogleVoice.
We tend to call friends and family in Mexico, France, Norway and occasionally Spain.

*Prices in pence per min incl. VAT*
Table	GoogleVoice	SkypeOut*
Mexico (Landline)	6.5	6.4
Mexico (Mobile)	12	20.7
Mexico-Guadalajara (Landline)	1.3	2.1
Mexico-Mexico City (Landline)	1.3	1.4
Mexico-Mexico City (Mobile)	12 ?	20.7 ?
Mexico-Monterrey (Landline)	1.3	1.4
France (Landline)	1.3	1.4
France (Mobile)	9.7	13.2
norway (Landline)	1.3	1.4
norway (Mobile)	13	13.8
spain (Landline)	1.3	1.4
spain (Mobile)	12	17.7

There's very little in it when comparing calls to landlines but Google Voice does seem to be cheaper when calling mobiles. I will check sound quality but unless it is way better than Skype, I will stick with the devil I know.

Getting Evernote to OCR for you

2010-08-06T15:34:00.004Z

Evernote is a great app that lets you make notes, take photos and screenshots, bookmark webpage and syncs everything so that you can access it from any computer, iphone or ipad. What I love about it, is that when you take a screen shot, it uploads the image to its server and tries to OCR the text, even hand-written text. Although technically speaking, Evernote doesn't actually do OCR:
"Evernote's image processing technology is a bit different. We analyze the image to generate a set of possibilities for each word that we see in an image. Each possible interpretation is given a score.
For example, we may look at a word and decide that this word may either be "clue" or "due", and we can assign a score to each possibility. This set of scored possibilities is stored in our database for searching.

As a result, there isn't a simple text representation that you can use. Instead, you can search our database to find the image based on the different sets of possible interpretations for each word."

Well, there is a way to get to that OCRed text (or data interpretation). You can find it in the files in Metadata/com.evernote.Evernote. Just in case anybody was wondering.

The long short communication of M. Stift

2010-06-03T11:01:00.005Z

Marc Stift also know as Stifty by some, has recently left Glasgow for the sunnier climate of Portugal. Just this week, the (not so short) short communication that he worked on tirelessly, has been published. I kept on trying to convince him that it was important that people understood the statistics of small sample size and that he should include the simulation graphs that he generated for determining the statistical power when determining the inheritance in tetraploids (but he ignored me). This is probably for the best as the figures would probably just have lingered in the depths of the supplementary materials. I am still working on convincing him to release those figures which might end up in his first blog or in a second paper. I'll keep you informed!

Increasingly wondering what publishers do for science and research

2010-05-31T08:57:00.006Z

It seems that researchers are increasingly using Open Acesss (OA) platforms like Arxiv or Nature Precedings to disseminate their work. Authors often submit their pre-print manuscript version to these sites or to in-house depositories, for example Enlighten at the University of Glasgow. Researchers are at least encouraged to do this by funding bodies and research institutions.
This often means that the article is in circulation before the publisher's nicely formatted version (see for example, Rod's Elsevier Grand Challenge Paper) and begs the question "What do the publishers do for research and the scientific process?".
Ten years ago, it was easy to see the role that publishers had, they disseminated your work by convincing libraries and individuals to subscribe to their journals. In this way, your research had a chance to be seen on a few library shelves across the world after a few months of format checking and page layout with the publisher. But now, the worldwide web does that for you and does it immediately!
O.K., publishers do play an important role in the review process. They make sure they get a famous and qualified editorial board who select good papers for review and choose good reviewers for the job. This increases the impact of the journal and so feeds back into the status of the journal and the publishers. But increasingly, this seems to be the only thing that publishers are providing and could be done by other institutions like universities.
It seems that publishers have caught onto the fact that things are changing fast and they need to do something about it. One solution is to enrich the readers experience of a paper if he reads it on the publishers website as opposed to the pre-print pdf version in these OA archives. This, I think, was the idea behind the Elsevier Grand Challenge and perhaps behind the PLoS Hub for Biodiversity . There is no doubt that we are in need of better ways of finding research and data with the ever increasing number of publications to keep up with.

A way to improve the commenting system on publications

2010-04-21T12:29:00.004Z

I was chatting to Rod a few days ago about his visit to CalAcademy for a Plos markup meeting and our disucssion strayed onto the commenting system of publications like Plos and the Biomed Central Journals. I was saying to him that I had left a few comments both as an individual and as a member of the molecular ecology discussion group in the department (not that I can remember the journal or the narture of the comments anymore) and that I had never received a response or feedback from the authors of the manuscript. Additionally, it isn't possible for me to get a list of the comments that I have left. Rod suggested that really what these sites needed was a way
to credit readers and commentors of the articles in a similar way to Disqus. Disqus is great, because all the comments you make on a range of different blogs and sites can all be accessed at Disqus, you can manage them yourself, edit them and delete them. You are in control of what
you have written. You can also see all the responses to your comments. Additionally, you get credits from fellow commentors for the comments and ideas that you put forward. It would be great if you could have the same level of control over the comments you leave on manuscripts at Plos and Biomed Central.
So I wrote a quick email to the guys over at Biomed Central:

Hi,
I was wondering whether there was a central page I could go to,
to see the comments I have left on manuscripts along with the responses to
those comments. If this doesn't exist, I think it should. Creating a system
of commenting like disqus might encourage more people to comment on articles.
It enables the commentor to keep track of their comments, receive feedback, get rated and thus gives an incentive to comment. You could just enable disqus on your site.

Kind regards,
Joseph Hughes

I got this in reply:

Dear Joseph Hughes
Thank you for contacting BioMed Central.
Readers' Comments are available to view on the right-hand menu of all published articles:
The link below will take you to an example article where a comment has been left, you can access the article by clicking the associated link in the right-hand menu:
http://www.biomedcentral.com/1471-2105/10/2
If you have any questions please don't hesitate to contact me.

Best wishes
David Roman

Either I was unclear or they just don't get it! In any case, I am very pessimistic about the system of commenting getting any better in the near future.

The people behind the paper

2010-02-05T14:36:00.004Z

I thought it might be interesting for readers to hear about how our recent paper came together and especially who the people are behind the names. A while back, samples of Halipeurus lice landed on Rod Page's desk. As a postdoc in his lab, I was charged with storing them in the freezer and entering the relevant data in the now defunct lousebase, although the data is now available on Google Docs.
Ruth Brown, a PhD student at the time working at the Zoological Institute London, had sent the samples, suggesting that it would be interesting to sequence them. The specimen came from the Trindade petrel (Pterodroma arminjoniana) on Round Island (near Mauritius) where she had been working for her thesis. The presence of this petrel on Round Island was probably a recent colonisation as there were no records of the petrel on the island prior to the 1960s.
I did not realize why it would be interesting to do this sequencing until I met Leandro Bugoni from Brazil. He was just finishing his PhD at the University of Glasgow with Bob Furness. He had been working on the Trindade petrel on Trindade Island (near Brazil). Interestingly, they had found little difference between these two island bird populations whether it was based on genetic markers, morphology or calls and yet they hosted different lice species.
We knew this thanks to the expert identification skills of Ricardo Palma based at the Museum of New Zealand Te Papa Tongarewa and whom I had collaborated with before on Pectinopygus lice on pelicans.
What we did not know, was how these two lice species were related, how divergent they were and their origin. Had they always been associated with the Trindade Petrel? Had they recently parasitized one of the bird populations?
Fortunately, a friendly Faroese MRes student, Sjudur Hammer, chose my suggested project proposal and did all the lab work. He copped very well in the lab and managed to get some good quality sequences for the Halipeurus lice from both islands.
And voila! We published what I think is a cool cospeciation study of lice and gadfly petrels and it was a pleasure to collaborate with such an international group of researchers.

Image searching

2010-02-04T12:29:00.005Z

I have been trying to find images on the web that will match images that I upload and I have come across a few cool websites.
To start with there is pixolu. Although it doesn't enable you to upload an image, it lets you search for particular key words and then select the types of images that you would like. Using these images, it then refines the search to find images similar to those that you have selected. I thought it was a very nifty tool. This is quite similar to Google Similar Image, except that it has a nicer interface and a lot of images in the Google Similar don't actually have a similar even though the same image in pixolu does.
Then there is retrievr which still doesn't let you upload an image but you can squiggle something in a box an it will find similar images on the web. I was impressed to find that when I did a very rough drawing of a tulip, the search did pull up an image of a tulip (see the screenshot).

But something like Gazopa was what I was really looking for. Unfortunately, it doesn't work as well as I would hope. Even though the image I upload is available on Flickr, it doesn't actually find it. It does do a good job at finding images with similar colours (see screenshot).

Species Image ReCAPTCHA

2010-01-14T10:26:00.005Z

After seeing the inspiring talk of Luis von Ahn on PopTech, I was thinking that CAPTCHA (Completely Automated Public Turing test to tell Computers and Humans Apart) could be a cool way to improve the OCR of species names in books OCRed by the Biodiversity Heritage Library particularly as Rod is currently using ReCAPTCHA on BioStor. BioStor is helping to annotate and extract data from BHL and Rod is using ReCAPTCHA to check that the annotation is being made by a human.
In my limited experience of OCRing, I have found that italicized species names are particularly hard to get right, so if ReCAPTCHA could be set-up to to use species names from BHL, then users annotating BioStor would be improving the OCRing of BHL articles and helping to annotate it.
Along the same lines, I have been thinking that it would be great if you could use the power of the brain to annotate species images that are on the web, a bit in the style of Google's Image Labeler which I find addictive so have been avoiding it for a while. Then quite by chance, I came across this image CAPTCHA at the University of Edinburgh.
I thought this would be a really cool way to help tag wildlife images at least using common names. You could also do a pro version for taxonomists with latin binomial tagging.

The facts about bottled water

2009-12-24T12:08:00.001Z

Presented by Online Education

Motion Chart of NCBI data

2009-12-09T09:58:00.005Z

The last decade has seen a huge increase in sequence data in public databases with an impressive increase in species coverage. Here, I have used Google's Motion Chart API and Google spreadsheet do illustrate the changes in numbers of sequences and numbers of species for different taxonomic groups. Whilst the nucleotide sequence increase against the number of species sequenced has been exponential for all taxonomic groups, the rate of increase in nucleotide sequences per species appears to have accelerated since 2007 for Fungi and Bacteria. The gap also seems to be widening between the number of nucleotides per species in the Metazoa compared the Viridiplantae. There appears to be no signs of a plateau and with the next-generation sequencers, we are likely to soon see an even sharper increase in the number of nucleotides per species. However, I suspect the rate at which additional species are added to NCBI might begin to slow as we find it harder to collect and sample novel species.

Berlin's eco-damaging styrofoam wall of dominoes

2009-11-10T09:11:00.004Z

It is rather disappointing that the Germans decided to celebrate 20 years since the fall of the wall by generating 1000 styrofoam dominoes. Styrofoam is one of the most ecologically damaging materials we create. Where are all the blocks going to go now? Probably into a land fill and take hundreds of years to degrade. It is surprising that a normally environmentally conscious country like Germany would not think of such issues.
They could have gone for something more environmentally friendly.

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Which digital photo printing is best?

2009-11-03T20:21:00.005Z

Following a previous blog and EditGrid spreadsheet, I got a comment about not including a quality comparison. Well Jon on the Gadget show has now done the job on 13 different companies. Colorama was a definite no no because the photos were all very faded.
Jessops got excluded but I missed the justification for it. OneView was the best but the most expensive at 73p per photo. So Jon chose Snapfish as the favorite because of quality and price.

Why I think a Phylogenetic Standard might not work

2009-10-23T09:21:00.004Z

Currently we have many different formats for phylogenies (e.g., nexus, newick, extend newick, phylip, xml) and there is no doubt that putting in place a Phylogenetic Standard would be a good thing but just because a group of researchers get together and decide that a Phylogenetic Standard would be good doesn't make it happen. Unless the phylogenetic community is behind the decisions being made which is unlikely to happen any time soon as phylogeneticist already have a poor record of submitting their phylogenies to databases like TreeBase.
These are obviously points that you are aware of as you mention them in your statement. I only remark that unless publishers enforce a particular format and submission of the phylogenetic data into repositories (like GenBank/EMBL), then however noble the idea of a Phylogenetic Standard is, it is unlikely to be put into practice by phylogeneticists.

Installing DBD::mysql on MacosX 10.5

2009-10-23T09:15:00.002Z

I was having real trouble installing DBD::mysql on my iMac (version 10.5.8) until I found this. So I updated my version of Mysql to Mac OS X 10.5 (PowerPC, 32-bit) from here following the instructions for updating from Marc Liyanage. And finally, it all worked. Thank you Marc Liyanage.

Pulling up text sections across multiple documents using searches and filters

2009-10-21T15:28:00.004Z

Came across A.nnotate.com whilst reading the comments here. In A.nnotate.com you can
search and browse the text, tags and notes
any part of the text can be annotated or even regions of an image
In the tools section, you can get an index of all the tags and you can also get a text file with the notes taken.
Unfortunately it is not free so I have only played with the example files and I am not sure my links will work but I thought it could be really good tool to integrate into BHL, GoogleBooks and Mendeley for example as it has the ability to pull up text sections across multiple documents using searches and tags so collaborators can mark-up pdfs and share their tags and notes.

Sense about science

2009-10-16T12:58:00.001Z

Wordle of keywords

2009-10-13T15:35:00.003Z

I have been monitoring my blog with google analytics for a couple of weeks and wanted to see what the main keywords were that had resulted in a hit on the blog.

It seems like a number of people have been looking for a iphone app that identifies bird songs. I wrote a while back a blog suggesting that a version of Shazam that had bird songs included would be really useful but as it turns out Shazaam doesn't really work that well when you have a lot of background noise which is likely to be the case when trying to identify birds from their songs in the wild. I will keep my eyes open for such an app as it seems a lot of you are interested. Likewise, if you here about anything, please leave a comment here.

Zotero linked into Mendeley

2009-10-12T09:26:00.003Z

Downloaded Mendeley 0.9.4 and now you can import all the references from Zotero. I didn't have too many refs in Zotero (844) so it didn't take too long to import them. After a couple of crashes, it now seems to work fine. I couldn't figure out how to import the pdf links unfortunately. I think this might be quite useful, especially as Zotero is so much better at importing the metadata.

Automating label print out from google lousebase

2009-10-09T10:57:00.005Z

I have been messing around trying to improve lousebase so that I can have tube labels automatically print out. The idea is that from within the lab, I could use an iPhone or any phone with a browser to add information to lousebase and then the tube identifier and information on which box,row,column I should put the tube in would be automatically generated by google spreadsheet.

So here is the form that you would point your mobile device (wireless laptop, iPhone, web enabled mobile)which should look something like this:

Loading...

This form is set-up so that when you add a new entry, a label is created on one of the sheets. If changes are made to the label sheet, I receive an email. I was hoping that the email would contain the changes so that I could automatically print out that email with an applescript called Pergamail, I found here.

Unfortunately it only says that changes have occurred on the page so I need to go back to the drawing board. I thought that maybe using the Google Data APIs would be useful but as I am behind a firewall, I think I might be entering a whole world of pain.

EndnoteX2, MacOS X and Word 2008 plugin

2009-09-15T14:15:00.002Z

After half a day figuring out a way to get EndnoteX2 to "cite while you write" I thought I would share my wisdom. There are a load of compatibility issues with word, macs and endnote, have a look here. But the most important thing they don't mention is that you need to update your version of word 2008 with the most recent service packs. You can find these here. Hope this helps.

Using Barcodes in Google Docs

2009-09-11T11:47:00.004Z

Barcode Software

Thinking of my future lab where I will have an iphone as a lab book to automatically update collection data in google docs and associate specimen tubes, extraction and PCR with barcodes that I will be able to generate and read with the iphone.

Lousebase on GoogleMaps

2009-09-02T10:44:00.000Z

No citation plugin for Mac in Mendeley => Using Zotero

2009-08-26T09:19:00.004Z

Mendeley still doesn't have a Word plugin for making citations. I tried for a while to sort out Endnote X2 with word 2008 and gave up. I followed all the suggestions I could find in the Endnote help and the EndnoteX2 submenu in word still didn't appear.
Zotero to the rescue. I installed Zotero version 2.0b6.5 and and the Mac Plugin for word 2008 and hey presto, it works! It works fine so it will do for now and I might be converted.

labmeeting.com

2009-07-30T08:37:00.002Z

What a rigmarole to signup to labmeeting.com. I had to send them a link to my webpage and then they asked me to put a link to labmeeting on my webpage and finally they let me sign up. It took 4 days!
If Mendeley took had the same strategy they wouldn't have 22,607 users with 2,723,657 articles. Couldn't find any stats for labmeeting.com
Pdf data extraction was just as bad in Labmeeting as in Mendeley. In labmeeting you can't provide a doi lookup.

last.fm versus spotify

2009-07-28T15:26:00.004Z

Last.fm suggests music that you might not have already heard off. Spotify relies on the fact that you know what you want to listen to.
You can find everything on Spotify, the tracks are a lot less extensive on last.fm, especially for classical music.
Spotify has ads in the free version.

Mendeley is getting better day by day.

2009-07-13T12:01:00.004Z

Unlike some cynics, I think Mendeley is the bees knees! I am currently collaborating on two separate projects and sharing the references thanks to Mendeley couldn't be easier. Now it is even better, with integrated pdf viewer and the ability to highlight and make notes directly on the pdf.
I am sold, I really think it is the best reference manager social networking tool out there.

My tag, my label = defining myself

2009-06-09T15:30:00.001Z

Wordle from my publications.

6"x4" digital print comparison

2009-06-09T14:13:00.003Z

Comparing digital photo online printing

2009-06-04T11:09:00.007Z

I have only compared the price of 6"x4" (15cmx10cm) digital photos here and included the all important delivery charge which usually varies more than the actual printing prices.

No. of prints	1-4	5-49	50-99	100-149	150-199	200-299	300-499	500+
Photobox
Price	£0.10	£0.10	£0.10	£0.10	£0.08	£0.08	£0.07	£0.05
Delivery charge	£1.49	£1.49	£1.49	£2.49	£3.99	£3.99	£4.99-£5.99	£7.99
Jessops
Price	£0.25	£0.19	£0.12	£0.12	£0.07	£0.05	£0.05	£0.05
Delivery charge	£1.49	£1.49	£1.49	£1.99	£1.99	£0.00	£0.00	£0.00
Snapfish
Price	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09
Delivery charge	£0.99	£0.99	£1.49	£1.49	£1.49	£1.49	£1.49	£1.99

Postage is additive for Photobox if you order a mix of calendars and posters or any type of mix. At Jessops, you can pick up your photos from your nearest store free of charge.

An the winner is Jessops for orders above 200 prints and Snapfish for orders below 150 and it is a close call between Jessops and Snapfish between 150 and 200 prints.

I will hopefully make a spreadsheet so that it is possible to calculate where you can get the best deal based on what you want printed. More of that later.

iPhone App to identify a bird song in the field

2009-04-23T14:13:00.006Z

Image by nixam via FlickrWouldn't it be cool if you could use something like Shazam to identify bird songs out in the wild. Doing a quick Google search, I found a few websites with mp3s of bird songs, for example xeno-canto. Shazam might already work with bird songs but I wouldn't know because I don't have an iPhone. I would get one though if I could use as a bird song identification tool.

UPDATE 30/07/2010.
I've found a few interesting posts and comments on this topic:
http://originalprojects.com/projects/shazam-for-birds
The comment by the user 'nature' is interesting http://www.tuaw.com/2009/02/09/this-iphone-app-is-truly-for-the-birds/
An education app http://itunes.apple.com/us/app/chirp-bird-songs-usa-lite-v3/id352826689?mt=8

UPDATE 05/05/2011

This blog posts explains in a neat way how Shazam works:

http://www.soyoucode.com/2011/how-does-shazam-recognize-song

Rod Page's Talk Science at the British Library

2009-03-19T09:33:00.004Z

Podcast of Rod Page's presentation for "Talk Science" at the BHL.

Mendeley profile and BiomedExperts

2009-02-26T14:26:00.003Z

Mendeley definitely seem to be on the ball, they have actually bothered to comment on my blog. They also seem to be very open about their future plans and about making certain aspects of their software flexible for use by the users (i.e. formatting of your own citations styles).
What I think would be a cool thing to do, is to use the information from the My Publications to automatically create peoples profiles.
In BiomedExperts, I only needed to select my publications to have a profile generated with keywords that define the organisms, concepts and ideas I work on. It also used my co-authors to create a network of collaborators and addresses from my publications to create a GeoNetwork.
My profile is bare at the moment except for My Publications. It would be nice if it could be self-generating.

Mendeley

2009-02-19T12:50:00.002Z

I have been doing a bit of a comparison between Mendeley and Papers recently because I haven't used Endnote for a while, actually since my last post on Reference managers. People suggected Zotero and EndnoteWeb to me, but I didn't like either of them.

I must say, I really love Mendeley as a social tool. It is great to be able to share pdfs with collaborators and to be able to access my references as easily at home and at work, especially since I have a PC at home and a mac at work.
Creating collections with all the associated metadata for publications is great. I haven't yet used the word plugin, so I will let you know shortly what I think of that. The down side with Mendeley is that you only have 500Mb of space online at the moment.

Papers is cool too, especially the fact that you don't need to open up a pdf reader as a separate program, you can do Google Scholar, ISI, Pubmed etc searches within Papers and automatically download pdfs if your instituion has access. You can highlight words in the pdf and do searches on those or highlight the doi and get all the associated metadata. Unfortunately, it only works and macs and doesn't have all the social networking aspect that Mendeley has.

Endnote, Connotea and GoogleScholar

2007-11-28T10:42:00.000Z

What's good about Endnote:
It helps to format bibliographies in 100s of different styles
It provides easy access to your bibliography
What's bad:
What's the point of downloading stuff to Endnote, it takes for ever. Wouldn't it be best to leave it on the web.
It's a pain to sort your bibliography, you end up with loads of different libraries and often want to merge libraries or split them.
It's a pain to add book references as you usually have to do it manually or any other non-journal references for that matter.

What's good about Connotea:
Easy to add new references, you just need a doi or URL.
You can reference anything that is on the web.
You can tag your references and see you else (how many other people) have that reference in their bibliography
You can find out about popular topics really quickly
You can add other peoples references to your bibliography
What's bad:
It doesn't enable you to use your references in your manuscript, you first need to download them to your reference manager

What's good about GoogleScholar:
You can easily get access to references and the associated pdf
Easy search for words, sentences
Books and books sections are available as well as reports etc..
Duplicated articles on the web are removed through clustering
What'bad:
You can't make your own library of interesting articles
You can''t use the references to add into your manuscript
You can't download the references

What do we need?
We need to find some way of sharing our bibliographies on the web (like connotea) so that people can avoid having to type in references manually (which is often necessary for book references in Endnote) and at the same time avoid having duplications of the same reference (like GoogleScholar clusters) and crucially be able to insert a reference from the web directly into our manuscript whilst writing without having to worry about downloading it to our reference manager, because there will only be one reference manager for everybody which will be on the web shared with everybody and tagged diffeently by all the different users.
I can't imagine this being to complicated to do, not that I would know how to do it. The most important thing would be to create a tool that can be added to Word or LateX that enables the linking to the web reference manager and formats the reference section of our manuscript according to all the different formats used by the journals.

Eco-friendly shop for radiator insulation panels

2007-11-27T16:10:00.000Z

I've been looking for eco-friendly shops to buy radiator insulation panels, I have come across quite a few new sites so I thought I would list them here:
CAPcarbon
earthwhile
ecomerchant
shopeco
ecotopia

Most of these site sell the same products and even use the same pictures, but prices do vary. It seems that CAPcarbon does not have a delivery charge which is good, but the cheapest price per insulation panel I could find (including delivery) was form earthwhile.

Good bye EQO, welcome TerraNet

2007-09-11T10:07:00.000Z

The future of mobile phone calls is peer-to-peer. Lets hope it works! I'm not sure how EQO is doing these days as I got fed-up with using it. It just didn't seem to work that well on my mobile and I couldn't convince enough friends to use it so it wasn't really worth it financially (see my previous post). I think the peer-to-peer system could work well but it ultimately depends on how many people use it. When you think of how many people share their wireless connection say in New York compared to here in the UK, you might in fact think that it will never work in the UK because we are too selfish. We will just have to wait and see.

Plastic Bag Petition

2007-09-05T10:02:00.000Z

People in Britain use an average of 300 plastic bags every year. Each bag lasts up to 400 years, spending the vast majority of that time in a landfill site or strewn across the British countryside. Have a look at dumped on channel 4 to see more scary statistics about how much we dump instead of recycling/reusing.

I have 5 cotton bags that I used when I go shopping and have been using for the past 2 years. It is great not to have a cupboard full of plastic bags and I feel much better walking home with my shopping in my cotton bags than in the orange Sainsbury's bags.

"In Ireland, a tax of 15cents per bag resulted in a 90% drop in plastic bag usage, and raised 3.5 million Euros which was spent on environmental projects." Now that sounds brilliant and if only the same could happen in Britain. I think it is important to show people where the tax-money is going, i.e. showing us that it is not just going into the government coffers and not being spent on environmental issues. It has to be visible improvements to make it easier for people to swallow more tax.

Please take a moment to sign the petition to introduce a similar tax (to be spent on environmental projects) of 10p per bag in Britain.

Carpenter/cabinet maker in Normandy

2007-08-16T13:41:00.000Z

This is a friend's site, he has made some really nice wooden libraries and beds. He works mainly in Normandy but travels around quite a bit for big renovation jobs. Great website!

EQO mobile: the way I see it

2007-07-09T14:21:00.000Z

Well it has markedly improved. It is easier to install and it doesn't use Skype anymore so you do not need to leave your computer running Skype.
But now you have an additional company to buy credit from instead of Skype credit. The other down side is that now you cannot IM for free Skype users sitting in front of their computers. You can only communicate for free with people who have installed EQO mobile on their phones and this is not entirely free as you have to pay your network provider for data transfer (unless you have an all inclusive deal). I think that EQO mobile has now lost interesting functionality. O.K. it was a pain to have your computer on all the time but at least you could communicate with the millions of Skype users. Additionally, the costs of EQO calls to Mexico for example are higher than they use to be with the Skype set-up.

Travel map

2007-07-04T16:37:00.000Z

Installing tesseract command line OCR on MacOS X

2007-07-03T12:22:00.000Z

Installing libpng from source:
http://kenno.wordpress.com/2006/04/20/compiling-libpng-for-mac-os-x/

fink install libjpeg, aspell, aspell-en

I will want to create my own aspell dictionary using taxonomic names:
http://www.mail-archive.com/code4lib@listserv.nd.edu/msg01545.html

Download and installing tesseract following install instructions:
http://code.google.com/p/tesseract-ocr/downloads/list

fink xpdf for pdfimages to extract images from a pdf:
>pdfimages -j LandPlants_paper.pdf LandPlantImg

To convert in imagemagick to tif for tesseract :
convert LandPlantImg.jpg -compress None test.tif

Using tesseract:
tesseract test.tif out.txt

I have now got a script to extract the names and check them against a dictionary of taxonomic names from spira.
I am thinking that using information from the article itself might provide even better results. When tesseract 2.0 comes out, there will also be a way of training the program to improve the character recognition. OCRupus also looks like an interesting program for layout detection but it doesn't work on MacOSx yet
The line extraction is proving to be much more difficult than first thought mainly because the lack of consistn format and the labelling at the nodes that get in the way of edge detection. I have tried a number of methods for cleaning up the image and bit by bit I will get there, I hope.

Advertising a holiday home for free on the internet

2007-06-12T12:03:00.001Z

It's not that easy to find sites that let you advertise your holiday home for free, but I have found a few and I have listed them here. By far the most practical is gumtree as you can actually put photos and links to your website.
Craigslist is almost as good as gumtree. I think it is still very much biased towards the US market.
Google base is quite handy but in most item listings there is an expiry date. I did find one category that did not expire.
Gite-directory is quite good too and the webmaster is very friendly. The submission and modification of info is not that straight forward unfortunately. The site does say it protects your email from spam and sends you any enquiry emails without problem.
I was very impressed with the self-catering-breaks site that makes it very flexible and easy for changing photos and general information. The enquiry email works brilliantly.
I would rate holidaylease second as it puts paid advertisers on the same page as your add, but it does provide a calendar for your bookings which can be quite handy.
Then, there is the whole range of local classified adds like loot.com and exchange.co.uk that let you put a few words on their site. They don't usually let you put a link to your website but they usually let you provide an email address. Unfortunately, I found that the add and email were hijacked on glasgow-times.com and diverted to another ad.
Freewebsitedirectory allows you to put a link to your website with a description line or two.
http://www.frenchentree.com/ is a new one that says you can advertise for free but it is very difficult for users to browser as it is overloaded with info and advertising.
The HomeIsAway website lets you advertise for free for one year. Either you pay for the link to your site or you provide a link from your site to theirs and you get the link for free. That defeats the point though.
rent-holiday-home does not let you put a link to your site but you can upload images and text and locate your property on a map.

Branch thinning and tracking

2007-06-07T14:54:00.000Z

I think I might have found a way to convert phylogenetic trees from image to nexus format through a process similar to that used in GIS map vectorization. This approach should also enable me to deal with trichotomies. The pattern matching approach that I had used previously turned out to be unsuccessful because of the many inconsistencies in tree drawing making it difficult to find a pattern that would always match a tip or a node. Line tracking offers hope!
All this would be so unnecessary if only researcher submitted their phylogenies to TREEBASE. Still, there are a number of phylogenies published prior to Treebase.

Thatched cottage to let in Normandy

2007-04-12T17:02:00.000Z

Here is a lovely cottage with 3 bedrooms available to let on a weekly basis during the school holidays or over long week-ends in low-season. It is beautifully situated next to a river in the quiet valley of St Denis le Thiboult in Normandy. The owners are always welcoming and know all the nice places to eat and visit nearby.
Lovely thatched cottage to rent in Normandy | Self Catering Breaks
gite cottage let normandy

OCR taxa names from phylogenies

2007-03-14T15:45:00.000Z

I have been trying out different open source OCR software, to recognise the taxa used in phylogenies. Tesseract (newly released by Google) did not fair as well as GOCR. If you train GOCR using a database of character images, it does even better.
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c(PICTURE)100 C. _asicus (14)
C. nasicus (_8)
C. jo_e_sjs (30)
C. co_fusoy (32)
C. coMfusoy (12)
C. su_cafu_us (_3)
C. su_cafu_us (68)
C. humey__is(_4)
C. vicoyiensis (_5)
C. p_y__lis (26)
C. vicfoyie_sÌs (54)
C. _ongi_e_s (16)
C. longi_e_s (19)
C. ve_osus (82)
C. veMos_s (166)
C. ve_osus (160)
C. ve_osus (149)
C. s__icivoyus
C.pe_lifus (131)
C. pellifus (151)
C. pellifus (192)
C. eleph_s (_18)
C. eleph_s (_13)
C. eleph_s (_16)
C. c___e (204)
C. cR_Re (205)
C. ca__e (208)
C. pyobosci_eus (58)
C. humey__is (56)
C. p_o_osci_eus (22)
C. scufel1_pjs (5)
C. nucu_ (117)
C. nucum (_43)
C. g____ium (_OO)
C. g__n_ium (gg)
Pakjsfan _p. (_1)
C. c__elli_e (49)
C. c__el_i_e (20)
__iica_ sp. (8)
C. p__yhoce_as (1)
C. p_y_hoceyas (16)
_______________________
GOCR using database option
_______________________
c(PICTURE)100 C. nasicus (14)
C. nasicus (28)
C. iowensis (30)
C. confusor (32)
C. coMfusor (12)
C. sulcatulus (23)
C. sulcatulus (68)
C. humeyalis(24)
C. vicoyiensis (25)
C. paydalis (26)
C. vicforiensÌs (54)
C. longidens (16)
C. longidens (19)
C. venosus (82)
C. veMosus (166)
C. venosus (160)
C. venosus (149)
C. salicivoyus
C.pellifus (131)
C. pellitus (151)
C. pellitus (192)
C. elephas (218)
C. elephas (213)
C. elephas (216)
C. cawae (204)
C. cawae (205)
C. cawae (208)
C. pyoboscideus (58)
C. humeyalis (56)
C. proboscideus (22)
C. scufel1aris (5)
C. nucum (117)
C. nucum (243)
C. glandium (200)
C. glandium (99)
Pakistan sp. (21)
C. camelliae (49)
C. camelliae (20)
Afiican sp. (8)
C. pyrrhoceras (1)
C. pyyrhoceras (16)

Installing GOCR using fink

2007-03-14T12:43:00.000Z

sudo nano /sw/etc/fink.conf
fink selfupdate
fink index
fink scanpackages
fink install gocr

Juicing apples

2007-03-08T18:25:00.000Z

Using Braeburns at £1.28/kg, I got 375ml from 0.740kg, so you get 0.5mL per gram. This means that 1L of Braeburn apple juice would cost £2.52 per Liter. That is quite a bit! Actually more than some pear juices. The juice was tasty, clear, tasting slightly like cider (farm-yardy/earthy).
Royal Gala, my personal favorite. Price of £1.18/kg. From 0.48kg, I got 325mL. That £1.75 per Liter. That's half the price of Braeburn and it is a much sweeter juice, it looks slightly pink, but maybe does not have such a strong apple flavour.

Syncing motorola L6 mobile with iCal and Google calendar: gcalsync doesn't work on my Motorola L6.

2007-02-13T14:25:00.000Z

This is how I want to sync it :
Contacts are sourced from my phone + Thunderbird at home
Calendar is sourced from Google Calendar when away + iCal at work + Thunderbird at home via ScheduleWorld
I only want to synchronize my mobile when I'm at home because I have bluetooth at home and don't want to have to carry around USB cables
I don't want to synchronize of WAP because I am cheap and my mobile network provider charges me for data transfer.

First use Spanning Sync to synchronize your Google Calendar with iCal.
Then use ScheduleWorld to sync Google calendar to Schedule World.
At home, install the TSync Thunderbird plugin for syncing the contacts.

gcalsync didn't work on my Motorola L6.

Technorati Tags: motorola, thunderbird, ical, macosx, XP, sync, scheduleworld

Juicing carrots

2007-02-12T19:22:00.000Z

I'm still trying to find the best fruit and veg to juice in terms of mL per pound. Carrots seems like quite a cheap veg to juice. For 463 grams of carrots (0.69/kg) I got 255mL, this means that it is £1.17 per litre. Almost half the price of juicing a pear.
On a related issue, did you know that the government is charging 17.5% on natural juice and smoothies whereas foods (burgers and ready-made pizzas) are not taxed. It doesn't quite seem right that good healthy juice is taxed the same as coca-cola. They are suppose to be encouraging use to eat and drink healthily.
carrots VAT tax juice smoothies

EditGrid for scientist

2006-11-30T16:35:00.001Z

Sharing data and results with EditGrid could be a biologists dream but will they ever want to share data in the same way as other researchers (e.g. economists or computer geeks)? There is no doubt that sharing scientific data would accelerate the pace of research especially in the slow moving fields like taxonomy and systematics. It is also important to put information into the public domain especially as most of the grants we are funded with come from the tax payer. See "Of lice and birds" for further details of my grand plan.

RSPB funds conservation of marshes in Poland

2006-11-29T10:17:00.000Z

The RSPB have yet a again made history. They are providing several thousand pounds to support the management of marshes in Poland that host 80% of the threatened species in Europe. It is a shame that we are having such an impact on the environment and continuing to inflict such destruction. I recently went to a lecture on the conservation of bumblebees. A little known fact is that 3 bumblebees have become nationally extinct due to man's pressure on the environment. Many more species are under threat. Unfortunately, these poor creatures that are vital to the functioning of our ecosystems (especially for pollination) do no receive the sort of coverage they deserve. A recently set-up Bumblebee Conservation Trust is trying to remedy this. Please be generous with your donations.
biodiversity climate change conservation

The forensic use of bioinformation: ethical issues

2006-11-02T12:04:00.000Z

My thoughts about the use of DNA samples and the National DNA Database which is the largest in the world.

List of questions

1. The interpretation of bioinformation

a. In your view, is the SGM Plus® system, which uses ten STR markers, sufficiently reliable for use in ascertaining the identity of suspects in criminal investigations and/or criminal trials?
No, Balding (1999) suggests using 11 STR markers and the FBI use 13. We should use as many as possible.

2. Sampling powers

a. From whom should the police be able to take fingerprints and DNA samples? At what stages in criminal investigations and for what purposes? Should the police be able to request further information from DNA analysts, such as physical characteristics or ethnic inferences?
The police should only be able to take DNA samples if someone has been cautioned or they have reason to suspect the person was involved in a crime. DNA samples should only be taken once the police have sufficient evidence to charge the person. The police should be able to request further evidence from the DNA analysts from the crime scene DNA samples if they have no other leads.

b. Should police expenditure on bioinformation collection and analysis be given priority over other budgetary demands?
No, police expenditure should be prioritised towards training more police and increasing wages.

c. Do you consider the current criteria for the collection of bioinformation to be proportionate to the aims of preventing, investigating, detecting and prosecuting criminal offences? In particular: is the retention of bioinformation from those who are not convicted of an offence proportionate to the needs of law enforcement?
No. The recent developments that enable police to take and keep DNA samples from anybody they stop, whether they are charged for an offence or not, is totally disproportionate to the aims of providing justice to society. DNA information should not be retained if the person is not convicted.

d. Is it acceptable for bioinformation to be taken from minors and for their DNA profiles to be put on the NDNAD?
No. Only if the minor is charged with an offence should the police be able to take a DNA profile and only if the minor is convicted should they be able to keep the DNA profile.

3. The management of the NDNAD

a. Is it proportionate for bioinformation from i) suspects and ii) volunteers to be kept on forensic databases indefinitely? Should criminal justice and elimination samples also be kept indefinitely? How should the discretion of Chief Constables to remove profiles and samples from the NDNAD be exercised and overseen?
No, it is not proportionate for either I) suspects or ii) volunteers bioinformation be kept indefinitely, nor should criminal justice and elimination samples be kept indefinitely. Volunteers and unconvicted suspects should be asked whether they want the bioinformation removed from the database after the case has been closed.

b. Is the ethical oversight of the NDNAD adequate? What, if any, research on NDNAD profiles or samples should be permitted? Who should be involved in the oversight of such databases and granting permission to use forensic DNA profiles or samples for research?
No, the ethical oversight does not seem to take into account the human rights of the person. The information is being treated as data without consideration to whom the bioinformation belongs to. A committee that includes representatives from the police, from human right organisations and ethical organisations should determine whether certain research should be permitted on the DNA profiles.

c. Who should have access to information on the NDNAD and IDENT1 databases and how should bioinformation be protected from unauthorised uses and users? Should forensic databases ever be made available for non-criminal investigations, such as parental searches, or the identification of missing or deceased persons?
Police detectives should have access to the information on the NDNAD and this information should be used for the identification of missing or deceased persons but only used for parental searches if it is a criminal investigation. Parental DNA tests in non-criminal investigations could be carried out by companies.

d. What issues are raised by the transfer of bioinformation between agencies and countries? How should such transfers be facilitated and what safeguards should be in place for the storage and use of transferred data?
The British government should be able to ensure that the bioinformation is not being kept by the foreign government, if the person is not convicted for the offence and data should only be shared with foreign governments if the person is a suspect in a criminal case.

4. Ethical issues

a. Is the use of DNA profiles in ‘familial searching’ inquiries proportionate to the needs of criminal investigations? Do you consider the use of familial searching may be an unwarranted invasion of family privacy?
No, ‘familial searching’ is an unnecessary invasion of family privacy.

b. Certain groups, such as ethnic minorities and young males, are disproportionately represented on forensic databases. Is this potential for bias within these databases acceptable?
No, this bias can put certain groups or minorities under greater suspicion.

c. Is it acceptable that volunteers (such as victims, witnesses, mass screen volunteers) also have their profiles retained on the NDNAD? Should consent be irrevocable for individuals who agree initially to the retention of samples voluntarily given to the police? Are the provisions for obtaining consent appropriate? Should volunteers be able to withdraw their consent at a later stage?

No, any volunteer should have an automatic right to withdraw their bioinformation from the database if unconvicted when the case closes. Keeping this type of data, increases the chance of ‘innocent’ matches and automatically increases the risk of suspicion against someone who was in the vicinity of a crime scene even if they were there several days before the crime.

d. Would the collection of DNA from everyone at birth be more equitable than collecting samples from only those who come into contact with the criminal justice system? Would the establishment of such a population-wide forensic database be proportionate to the needs of law enforcement? What are the arguments for and against an extension of the database?
Yes, the collection of DNA of everyone at birth would be more equitable, but it would NOT be proportionate to the needs of law enforcement. There are in my view absolutely no arguments for the extension of the database. Civil liberties and human rights are central to the democratic process.

5. The evidential value of bioinformation

a. What should be done to ensure that police, legal professionals, witnesses and jury members have sufficient understanding of any forensic bioinformation relevant to their participation in the criminal justice system?
Education must be improved so that all strands of society have a better understanding of forensic bioinformation. Courses on DNA forensics and the necessary statistical tests used should be provided to police, legal professionals, witnesses and jury members so that they can make informed decisions in a court of law.

b. How much other evidence should be required before a defendant can be convicted in a case with a declared DNA match? Should a DNA match ever be taken to be sufficient to prove guilt in the absence of other evidence?
A DNA match should never be taken alone as evidence of guilt. Proof that the person was present at the time of the crime and motive for the crime should be prerequisites.

6. Other issues

a. Are there any other issues, within our terms of reference, which we should consider?
Citizens should be able to know at any one time, the bioinformation that is being kept on them and the reason why this bioinformation is being kept.

freedom DNA bioethics forensic liberty ID

Colliding galaxies: beauty!

2006-10-17T15:51:00.000Z

Reduce, re-use, recycle

2006-10-12T12:29:00.000Z

As anybody seen the TV program "It's mot easy being green". They should have used this as the sound track.

New mouse species on our doorstep.

2006-10-12T09:48:00.000Z

It is not often that a new mammal species is discoverd in Europe. After careful comparisons of the different mice species on the island of Cyprus, Bonhomme et al. (2004) considered the Cyprus mouse to be sufficiently different to the other known mice in the region to name it as a new species: Mus cypriacus. Sorry, but can't find a photo.

Punk finch

2006-10-11T13:33:00.000Z

A multicolored punk finch (Atlapetes latinuchus yariguierum) has been named as a new bird species in Columbia. It is not often that scientists discover a new species of bird.

Best pears to juice

2006-10-06T11:11:00.000Z

I have recently bought a juicer and have been testing which pears are best for juicing.

2 Conference pears weighing 480g provided 300mL of juice: 0.62mL/g at a price of £2.40/L
The juice was sweet, creamy but not powdery and gave an olive green colour.

2 Comice pears weighing 510g provided 375mL of juice: 0.73mL/g at a price of £2.36/L
The juice was thick with small bits, pulpy, sweet and a muddy brown colour.

2 Williams pears weighing 285g provided 125mL of juice: 0.43mL/g at a price of £3.47/L
Very thick juice almost like a smoothy, strong pear flavor with a creamy brown colour.

I would suggest using Comice pears for juice as they provided the most juuice per gram although Conference pears are probably just as good as they are usually a bit cheaper so the price per mL is very similar.

Skype on your mobile=> EQO

2006-09-22T09:22:00.000Z

O.K. I have now used EQO to phone a landline in Mexico city, these are the details.
Virgin mobile, my mobile carrier charged me the following:
21:52:29 Accessing other sites £0.03
21:52:29 Accessing other sites £0.04

I think these two separate charges are for the initial connection to EQO and then the actual call.
The call didn't last but here are the Skype details:
21:55 SkypeOut to my mobile for 00:00:45
21:55 Skypeout to Mexico city landline 00:00:36
With a cost of £0.1548
The total cost to phone a Mexico city landline from my mobile using EQO and Skype for 36 seconds was 22p, calling using my Virgin carrier would have cost 80p.
EQO Skype mobile Motorola L6

EQO revisited

2006-09-21T11:11:00.000Z

Well, I managed to install EQO on my motorola L6. I use virgin mobile but as this was not an option as a carrier, I selected T-mobile as Virgin piggybacks on T-mobile. Installation was straight forward although I had to install Opera mini onto my mobile as the virgin browser wasn't letting me download EQO.
Installation was not to bad but the pricing system is far more complex. I phone France for 1 min and these are the pricing details:
Virgin charged me twice for data transfer
21-Sep-06 10:41:28 Accessing other sites £0.03
21-Sep-06 10:41:28 Accessing other sites £0.07
And Skype charged me twice:
21/09/2006 10:42 My mobile 00:01:02 duration
21/09/2006 10:42 France, Landline 00:00:47 duration
This cost me €0.22=£0.14
TOTAL COST of £0.24
This is mainly the cost of the SkypeOut from my computer to my mobile for the initial connection (£0.166 including VAT). I've actually been charged a bit less.
Calling France would normally cost me £0.40 per minute with Virgin.
EQO seems a bit cheaper. Next time I call, I will spend a bit more time on the line and I will report back to you. I think that if Skype and EQO got together to give more appropriate information about pricing, they might get a few more people interested.
mobile EQO Skype motorola L6

EQO pricing

2006-09-20T13:03:00.000Z

With virgin mobile the cost of data transfer is 0.5p/kb and apparently with EQO it wuld be possible to make over 100 calls with 1Mb of data transfer. This would mean approx 10kb for 1 call, i.e. with my mobile provider this would cost me 5p. Then, we need to add the cost of the SkypeOut call to your mobile to make the initial connection, this will cost an additional 15p.
The rest is priced as follows:
- For an incoming call to your EQO wireless Skype phone from a Skype buddy there will be no additional charges.
- For an outgoing call to your Skype buddies there will be no additional charges.
- For an outgoing call to a landline or cell phone you will be charged the appropriate Skypeout rates on top of the Skype out rates for the incoming call.
So it would cost me a bit more than 26p to make a 1 min phone call to a landline in Mexico and an extra 6p per additional minute. Whereas phoning Mexico without using EQO and SkypeOut would c ost me 80p per min. I think it could be worth it. I will see whether I can install EQO on my Motorola L6.
EQO Skype mobile motorola L6

New species in Indonesian water

2006-09-18T13:49:00.000Z

Amid all the recent tragic news about disappearing species, scientist have managed to find approx. 20 new marine species in Indonesia.
Lets hope that Conservation International manages to protect the area before these very localised species disappear.

Technorati Tags: diversity "new species" discovery wildlife

More obese in the world than starving people.

2006-08-15T10:38:00.000Z

I find this BBC news article particularly worrying but unlike the scientists who carried out this research, I don't think that subsidies for fruit and veg are going to change anything. Rather, the companies which produce foods that cause obesity or have any known effects on human health should be heavily taxed and the money directed towards the hospitals and sport centers.

EQO and EpyxMobile

2006-08-08T16:18:00.001Z

Image CC Thomas Favre-Bulle

In an effort to find out whether it was possible to use a bluetooth enabled mobile as a headset for Skype, I have come across some interesting software.
The clever EQO software which you need to install on your PC and your phone enables you to phone from anywhere to anywhere for SkypeOut prices. If I understand correctly, when you make a call to a Mexican landline for example, EQO software on your mobile contacts your computer via some EQO server, for this you will be charged by your mobile carrier for data transfer, then EQO on your PC uses Skype to SkypeOut to the Mexican landline and then SkypeOut to your mobile so essentially it will cost you 2p + carrier data transfer cost to phone Mexico from your mobile.
But really what I am looking for is a way to have something similar to BT fusion, i.e. a set up that would enable me to call for Skype prices when I am at home using my mobile so that I don't need to use a headset and don't need to be in front of the PC.
Now EpyxMobile is close enough to what I wanted as you can see from this Skype article for mobiles. Unfortunately, I have been unable to download the free software for the time being so have been unable to test it. Sorry!

Skype mobile EQO bluetooth

Curious George!!

2006-08-02T10:59:00.000Z

Networks of species.

2006-07-27T09:35:00.000Z

By evaluating the role of a species in an ecosystem such as its position within the network of species in the community/ecosystem and thus the stability that it provides to the community, we could evaluate the importance of that species. The loss of some species on the periphery of the food web might have a much lower impact than central species that are interconnected with large numbers of other species. This still makes it bloody hard to put a £ value on a species but at least they species could be ranked in order of importance within the ecosystem. Then again maybe not?
diversity
conservation

Beckett in rebuke to US over Scottish stop-off for Israeli bombs

2006-07-27T09:25:00.000Z

I think it is great that someone in the government, i.e. Margaret Beckett, is standing up to the US and lets hope that we continue to distance ourselves from the terrible US foreign policy. I think that we should publicly deny the US request for 2 further stopovers at Prestwick in the weeks to come. This would demonstrate that we are not their lap dog and that we do not support their foreign policy. Also, we would not be seen as hypocrites, helping Israel bomb Lebanon while sending humanitarian aid to Lebanon.
Hezbollah
Israel
Lebanon

Public opinion polls on the war in Lebanon

2006-07-26T14:10:00.000Z

Only 22% of Brits believe Israel has reacted proportionately to the kidnapping of soldiers..

64% of Canadians back Israel's unjuste war in Lebanon.

43% of web opinion think Israel's war on Lebanon is unjustified.

28% of British voters back Palestinians versus 14% supporting Israel

Israelis still overwhelmingly back the war, with 90 percent wanting it to go on until Hizbollah is driven from southern Lebanon

59% of Europeans interviewed describe Israel as the top threat to world peace ahead of North Korea, Afghanistan and Iran.

69% of Lebanese and 98% of Egyptians are against the United States policies and the country as a whole.

20 out of 23 countries think that Europe would do a better job than the US in world affairs.

66% of a French opinin poll was against the invasion of Iraq before the war started.

Biodiversity information: where is it all?

2006-05-19T15:36:00.000Z

Finding information about species at a particular location (continent, country, region) is almost impossible. Why? Because that information is behind the closed walls of our natural history museums worldwide, usually inside ancient journals, on little paper cards or pinned in huge specimen cupboards. How much of it is digitilised? I wouldn't know, the museums do not readily share their information with the general public, eventhough it is us who pay for the work they are doing.
Unlike the "Vase with twelve sunflowers" by Van Gogh which is worth over $39,921,750, it is difficult to put a price on a species or biodiversity. Why is it easier to put a price on a painting than on the sunflower species, Helianthus annuus? I think that is only once we start releasing the information that naturalists, ecologist and systematists have gathered on the millions of species which we know about, that we will begin to be able to put a value to the diversity of life on this planet and then at last we will be able to protect the planet's biodiversity.

Buying a flat in Scotland

2006-05-05T15:18:00.000Z

This is the first in a series of blogs about buying flats in Scotland. In Scotland it is really quite different to England and Wales. The offers over pricing system is a real pain! This is always the lowest amount that you can pay (as opposed to the value that the seller would like to get, like in England) and when the property comes to a closing date with blind bids from other interested parties, the sold price can be way above the offers over price. This makes it difficult to know the relative value of property especially as estate agents always try to bump up the price by pretending that lots of people are interested.
I have started to wonder whether as a first time buyer, I might be better off waiting until prices stabilise or come down but before leaving the game, I feel it is my duty to give a bit of guidance to first-time buyers. So come back to this site soon as I will be giving you the prices at which properties were put on the market, the price at which it sold and the schedule for a number of properties in Glasgow. Hopefully, this will be usefull for determining what offer to put on a property when it is on the market at offers over.

Nuclear Power. No thanks!

2006-04-28T11:39:00.000Z

I'm getting really worried that the government is seriously thinking about nuclear power. They are even suggesting that to get rid of nuclear waste, they bribe communities to bury the waste under their houses. The waste will only be safe after more than 100 years. The government is so thoughtful. They only think of the immediate future: the next election. Who cares about the next generation?
We could be taking a central role in the development of clean, renewable sources of energy and lead other countries by example but Tony Bliar prefers to follow the gringo way, i.e. lets pollute the planet so that the next generation can't survive on it.

Switching to Gizmo: Is it worth it!

2006-04-13T15:55:00.000Z

I thought I might use Gizmo instead of Skype because it uses SIP which is open source enabling communication with other SIP software such as X-Lite Softphone, it works fine and even looks very much like Skype. With Skype, you can only Skype-to-Skype whereas with Gizmo, you can Gizmo-to-XLite or Gizmo-to-IM. I think that by hidding the portocol that Skype uses for VOIP, it is stopping the expansion of VOIP and monopolising a market in which it has a strong-hold. Other software like Gizmo use an open source protocol and work just as well as Skype.
I am considering changing so have compiled price comparisons for Skype, VOIPcheap and Gizmo for countries I call on a regular basis.

*Prices in pence per min incl. VAT*
Table	VoipCheap	SkypeOut*	Gizmo
mexico (Landline)	2.25	6.28	6.67
mexico (Mobile)	3	6.28	6.67
Mexico-Guadalajara (Landline)	2.25	1.98	1.62
Mexico-Mexico City (Landline)	2.25	1.36	1.62
Mexico-Mexico City (Mobile)	3	6.28	2.75
Mexico-Monterrey (Landline)	2.25	1.36	6.67
france (Landline)	free	1.36	2.75
france (Mobile)	10.5	12.9	14.74
norway (Landline)	free	1.36	3.31
norway (Mobile)	12	13.51	13
spain (Landline)	free	1.36	2.18
spain (Mobile)	15.75	17.26	18.14

* Rates mentioned are per minute, and calls are rounded up to next minute.
your billing address is in the EU, you will be charged 15% VAT when you buy Skype Credit.
However, the calls will be shown on your call list and your account will be credited exclusive of VAT.
At the moment it is not really worth me changing completely, but I will use Gizmo when phoning Mexico city mobiles. That is the advantage of VOIP software, is that you can so easily switch from one company to another for calling different countries.

How to make your city flat greener.

2006-03-29T12:37:00.000Z

I was inspired by the program "It's not easy to be green"; on BBC2 yesterday but was thinking that it is much easier to be green in the country when you have loads of space. In the city it is not possible for a flat owner to build a water wheel or have solar panels. I suppose you could have solar panels but all the flat owners in the block would need to agree. It is a shame that the government and city councils are not encouraging home owners to be a bit more green. There is only so much we can do: energy saving light bulbs, water saving flushes, taps and shower heads, recycling paper, cans, glass and plastic at your local supermarket. However, when it comes down to producing your own electricity or recycling grey water, it is not really feasible if you live in a city flat.

Still, I have been looking for products that are energy efficient and water saving and here goes (CAREFULL not all products on the sites are necessarily energy saving):

Household equipment for saving water and energy-saving light bulbs
http://www.neco.com.au/default.asp

Energy saving light bulbs
http://www.light-store.co.uk/catalog/index.php/cPath/3
http://www.electricbikesdirect.co.uk/productlist.asp?category=8
http://www.maplin.co.uk/family_free_delivery/Energy%20Saving.htm

Garden compost and rainwater collection
http://www.trycomposting.com/sww/index2.htm

Range of water-saving taps, shower heads and toilets flushes
http://www.niagaracorporation.co.uk/index.php?action=shop
Tap inserts to reduce flow
http://www.tapmagic.co.uk/products.html
Bathroom products
http://www.thomasdudley.co.uk/water_saving.asp

Everything from Eco Kettles to water-saving flush
http://www.proeco.co.uk/
http://www.shopeco.co.uk/

Lots of energy saving gadgets:
www.ecotopia.co.uk

Only two steps away from the chinese surveillance system

2006-03-01T16:53:00.000Z

It seems that Blair has been looking to China's survelliance system for inspiration. Imagine if the Ntional Identity Registry was accepted and made compulsory, we could do exactly what the Angry Chinese Blogger is talking about. Scary world we're living in!

Technorati Tags: NO2ID, ID card, ID cards

Dispatches: stealing freedom

2006-03-01T15:38:00.000Z

It is about time we heard about the role the government is taking on ID cards. I thought the Dispatches: stealing freedom was quite balanced in its approach. It is a shame that there is not a bit more talk about the ID cards and the National Identity Registry in the media. I am afraid that once again, the government and its whips are going to manage to push through another legislation that will take away our freedom like the last time. It is now illegal to demonstrated within a mile of Westminster and if you do, you can be searched and finger printed under the Prevention of Terrorism Act 2005. The guys and girls in blue seem to be using this to search and arrest anybody that gets in the way especially if you are voicing your opinion against the government.
I have written to a couple of peers about the 6th of March ID card bill that is going through the House of Lords. I am glad to see that I am not the only one. Well done CuriousHamster. I hope that this issue picks up a bit of momentum in the blogosphere before it is too late. I think it is imperative that the House of Lords stand by their re-amendments. I really hope they do.

See how big Blair's nose gets when you pull it!!!

Technorati Tags: ID cards, freedom, terrorism

No2ID cards.

2006-02-28T15:40:00.000Z

ID cards are wrong. I am a sovereign citizen and I do not live by permission of the government. The government should be the servant of the people and I should not be its servant. I have the right to my privacy and my freedom and the government has no right to take them away from me. It is not the role of the government to engage in the surveillance of all of its citizens. Maybe the few citizens that have broken the law or are likely to break the law but NOT every single citizen. The National Identity Registry is the main problem with the governments proposal: I will become a number and more and more personal information such as spending habits, ethnicity, religion, sex preference, health records, criminal records, driving records will be linked to it.
These cards seriously threaten my freedom! Join me and say no to ID cards.

Technorati Tags: freedom, ID cards, trust, NIR

Blondes had a selective advantage 10,000 years ago?

2006-02-27T15:05:00.000Z

I read a recent article in the Times suggesting the diversity of hair colour arose some 10,000 years ago and that blonde hair was a selective advantage for women. I have gone to the original scientific publication (Evolution and Human Behavior, Volume 27, Issue 2, Pages 85-168, March 2006) because I was intrigued at how they measured that this trait arose prior to 10,000 years ago. Essentially, it seems that sexual selection must have played a role in Europe as humans moved further north 35,000 years ago. The women became more reliant on the men for food and men having to hunt further away from home were more likely to die probably resulting in a higher proportion of females competing for the males attention, thus colourful hair being an advantageous attention-seeking trait.

It turns out that the molecular data gives a rather different date for the origin of the hair colour: "Harding et al. (2000) have investigated this evolutionary scenario and found that the time to the most recent common ancestral hair color would be about a million years, with the redhead alleles alone being approximately 80,000 years old. Templeton (2002) has come to a similar conclusion: If the cause were relaxation of selection, the current level of hair-color diversity would have taken 850,000 years to develop."

The more rapid evolution suggested by the anthropologist Frost is a result of positive selection (rather than relaxation of selection being the cause for polymorphism in hair colour).

Performincing from Firefox to Blogger

2006-02-27T11:18:00.000Z

I have been trying to figure out how blog to blogger using Performancing extension in Firefox. Solutions Watch give a good explanation of how to set it all up: Blog from Firefox with Performancing for Firefox
Performancing have also added functionality for Technorati Tags making it really easy to add tags to your blog.

/>
Technorati Tags: internet, blogspot, blogging

2006-02-17T10:18:00.000Z

Blog posting from Gmail

I think I have figured out how to post a blog with hyperlinks and pictures that are on a server. I found this site useful. Essentially you need to write an html file in a text editor and save it as a .html file. You need to set up you blog to automatically publish the emails that are sent to it. Then you attach the .html file an send it without any body text or subject to your blogspot. I use Flickr to post pictures by pasting the html into the website. I would be grateful to anybody out there who has figured out an easier way to post emails containing pictures and hyperlinks on their blog.

I am also trying to figure out a way that I can send the emails or post the blogs at a specific time. At the moment I am usiing iCal on my iMAc to send an email automatically to my blog, but this does not allow me to attach hyperlinks or pictures. Any advice or help is very welcome

The taxonomy revolution

2006-02-16T11:52:00.000Z

The way we do taxonomy (and to a certain extent systmatics) hasn't changed for over 200 years and yet other sciences (Is taxonomy a science?) have changed tremendously in several decades, think of the field of genetics for example. I believe this is because genetics has embraced a range of new technologies whereas taxonomists are set in their ways and any changes to the way they do things are fought against even if the chanes could make their work more efficient. One particular example, is the way they have fought against DNA taxonomy which in my view could provide a very valuable technology for sorting of large numbers of unknown specimens prior to more traditional morphological species identification and naming (see the barcoding of life initiative).
Other technologies that they have been slow to embrace, are the web and oline publishing. The web provides an ideal working platform for a field like taxonmy as it enables the dessimination of work across the world instantaneously. Rather than needed to travel across the world to search through publications and specimens draws, the web and online publishing could facilitate the sharing of information.
I think this is a topic that will be blogged sporadically as it is dear to my heart.

Problems with postdoc supervisors

2006-02-15T20:21:00.000Z

Have a read of this article, it will give you an idea of how to choose
a postdoc
supervisor who will be essential for your future in academia.
link

The life of a postdoc.

2006-02-15T15:06:00.000Z

Being a postdoc can be bloody hard. Not knwoing what will be next and
whether there will even be a next job is probably the most depressing
thing. Funding is never easily obtained even though postdocs are the
backbone of research these days. It seems that the number of PhDs
continues to increase, whereas the faculty positions for us to go into
have not. link

I think that a revolution in the way academia is run is desperatly needed.
First, I would suggest that some security is provided to postdocs, by
that I mean a salary provided by the government so that postdocs can
continue working until they are awarded a grant or fellowship. This
would save us from claiming unemployment and at the same time give us
the financial support we need to continue our work.

Secondly, the countries like France that force postdocs to go abroad
should provide garanties for reentries to their homeland link

Thirdly, most importantly we need to be listened to. For that I
suggest that we form a postdoc union so that we can collectively
bargain for issues specific to postdocs. The postdocs at the
University of Connecticut Health Center have already gained status as
both employees and trainees as well as improved pay and benefits link

If a union of european postdocs (Europan Postdoctoral Association)
could be built, we might improve our plight.

I am really interested in knowing of anybody you feels the same way
and anybody you knows about setting up such a union.

Religious cartoons.

2006-02-11T11:51:00.000Z

I have been debating this with a pakistani friend, french friend and scottish friend. All had very different points of view. The whole issue really made me think about the chapter on comedy in Status anxiety a book by Alain de Botton. Essentially, he explains that the cartoons that were drawn of kings, queens and Napoleon have the aim of bringing about change. In hist words: " The underlying, unconscious aim of comics may be to bring about - through the adroit use of humour - a world in which there will be a few less things to laugh about."
I think the cartoons that have been recently published of the prophet Mohammed are just trying to improve the way we understand one anothers culture and I hope that the people that have seen these cartoons as disrespectfull can attempt to see the funny side of some of the cartoons.

Chat within Gmail:

2006-02-11T11:40:00.000Z

I love it. It is just so easy to use. Google is really in a league of its own. Still it is a bit scary how much information they are gathering on us.

What is karma!

2006-02-10T16:34:00.000Z

Well this is a good definition:
http://en.wikipedia.org/wiki/Karma

but I prefer the following poem that explains it well:
"Each thought, each word and each deed
has to be accounted and compensated for in Nature.
Every cause has an effect and every action brings about a reaction.
Uproot the cause and the effect disappears.
This has been done by the Masters
who have transcended these laws..."
- Sant Kirpal Singh

I think the idea of having a balance in Nature and everything we do,
is central to much of the research life scientist do. They try to
understand why species are kept in check and how ecosystems stay
stable. Critically, in this time of change where humans have had and
are still having a huge impact on the environment, life scientist are
trying to understand how the balance in Nature could return and
stabilise before we go extinct. "Every action brings about a
reaction". We know that we are the cause of climate change but for its
effect to disappear we really need to start changing our behaviour.

And there was life!

2006-02-10T16:08:00.001Z

But it didn't happen all at once and took far more that seven days.

What a cool thing!

2006-02-10T16:08:00.000Z

Its cool once you figure out all the ins and outs!

"Louis, I think this is the beginning of a beautiful friendship." Quote from Casablanca (1942).