Σεισμικές ερευνες για ανεύρευση υδρογονανθράκων

Οι έρευνες αυτές που γίνονται μέσω εξαιρετικά δυνατών ήχων χαμηλής συχνότητας (παράγονται μέσω εκρήξεων πεπιεσμένου αέρα κάθε 5-10 δευτερόλεπτα και θα διαρκέσουν 3 μήνες!!! για αρχή...) έχουν ξεκινήσει εδώ και ένα μήνα. Δυστυχώς η χώρα μας (ΥΠΕΚΑ), παρά την έγκαιρη και επίσημη ενημέρωσή της από τις οργανώσεις WWF Ελλάς, MOm, Tethys Research Institute και Ινστιτούτο Κητολογικών Ερευνών Πέλαγος δεν έλαβε κανένα μέτρο προστασίας των πληθυσμών κητωδών που κινδυνεύουν και ούτε καν απαίτησε από την εταιρεία που κάνει τις έρευνες, ή έκανε μόνη της και ανεξάρτητα, μια Μελέτη Περιβαλλοντικών Επιπτώσεων. Τα δε μέτρα που δέχθηκε να λάβει η εταιρεία (ένας οπτικός και ένας ακουστικός παρατηρητής κητωδών στο σκάφος για να καλύπτουν ...όλο το 24ωρο) είναι αστεία και αποτελούν μόνο βιτρίνα, δεδομένου ότι η ίδια εταιρεία εφαρμόζει πιο αυστηρά μέτρα επιτήρησης σε άλλες χώρες. Με βάση την συμφωνία ACCOBAMS που έχει υπογράψει και επικυρώσει η χώρα μας, οι έρευνες δεν έπρεπε καν να γίνουν στις σημαντικές περιοχές για τα απειλούμενα κητώδη (όπως έχει χαρακτηρίσει η ίδια η ACCOBAMS την Ελληνική Τάφρο - δείτε: το link για τις προστατευόμενες περιοχές ), αλλά και όπου θα γίνονται θα έπρεπε να υπάρχουν μελέτες επιπτώσεων και να παίρνονται όλα τα μέτρα προφύλαξης με αυστηρά πρωτόκολλα και τουλάχιστον 7 παρατηρητές πάνω στο σκάφος, που να σταματούν τις εκρήξεις όταν εντοπίζουν κητώδη σε κάποια απόσταση από το σκάφος. Οι επιστολές του Ινστιτούτου Κητολογικών Ερευνών Πέλαγος και ο θόρυβος που δημιούργησε η επερώτηση ενός ευρωβουλευτή ευαισθητοποιημένου στα περιβαλλοντικά θέματα έχουν δημιουργήσει σημαντική πίεση προς την κυβέρνηση και μοιάζουν να μπορούν να φέρουν κάποιες αλλαγές στο σχετικό νομοθετικό πλαίσιο τουλάχιστον για κάθε μελλοντική σεισμική έρευνα στον Ελληνικό χώρο. Η βοήθεια που μπορεί να προσφέρει η μαζική υπογραφή του ψηφιακού ψηφίσματος, μπορεί και αυτή να αυξήσει σημαντικά την πίεση διεθνώς. Σας καλώ λοιπόν όσους και όσες συμφωνείτε, να υπογράψετε το σχετικό ψήφισμα:

Sign the Petition to save endangered whales from seismic surveys in the mediterranean http://www.thepetitionsite.com/407/827/247/save-endangered-whales-from-seismic-surveys-in-the-mediterranean/

Just keep swimming..

Great News with my Cephalopod beaks analysis.. I'll write more about it soon.. Until then..

Pelagia @ Pelagos

For those who don't know me well... my name is Pelagia and I love the Pelagos (the sea)! I am officially a Marine Scientist, since I have completed my MSc in the University of Glasgow in Marine System Science, with merit! :) I will start writing about my volunteering experience in Pelagos Cetacean Research Institute which so far has given me so much knowledge about cetaceans in Greece.

Pelagos is a is a scientific non-profit organisation located in Athens - Greece, studying the conservation of cetaceans in the Mediterranean and mostly those that live in the Greek seas. The main goal of Pelagos Institute is to inform and educate as many people as possible to Greek natural heritage and especially dolphins and whales. During my volunteering experience in the past month, I have learned a lot about cetaceans and the research methods that are used, which help us know so much about those magnificent animals. Dr. Alexandros Frantzis and Voula Alexiadou have both been very welcoming. I have been learning so much from their experience and knowledge on the field. The amount of work and effort they have been doing all those years is of great importance; therefore I believe that the world should know more about it. During the last few weeks I have only helped a little with the identification of Cephalopod beaks, highly representing in the diet of Sperm Whales. Cephalopod beaks and other hard prey remains are frequently used to study the diet of cetaceans. It is amazing how we can use the beaks to identify certain species and calculate the squid's size. So far I have been trying to identify the differences in the lower and upper jaws of possible families: Histioteuthis, Octopoteuthis, Ancistroteuthis, Onychoteuthis and/or Chiroteuthis. It has been a great experience, while learning so much and I will be updating my blog with more exiting facts I discover every month. ><> ><> ><> ><> ><> ><>><> ><> ><> ><> ><> ><> ><> ><>><> ><> ><> ><> ><> ><> ><>><> ><> ><> My cetacean observation: Common short beaked dolphins - Zakynthos island - Ionian sea, Pegasus cruise, location: Gulf of Laganas, Date: 24/07/2010, Time: 16.00 ><> ><> ><> ><> ><> ><> ><> ><>><> ><> ><> ><> ><> ><> ><> ><>><> ><> ><> ><> ><> ><> ><> ><>><> ><> ><> ><> ><> Any questions?? I'll be more than happy to answer them!! Just feel free to contact me through this blog! Cheers! :) ><> ><> ><> ><> ><> ><> ><> References: Pelagos Institute website - A.Frantzis, G.Paximadis, V.Alexiadou ><> ><> ><> ><> ><> ><> ><> ><>

Dancing in the water..

Here's what Greek waters have to offer... The feeling you have when watching these marine animals dancing in the water cannot be described with words...Enjoy!

Biology & Computer Science are getting married!!

New Way To Store Information Via DNA has recently been discovered. Seems like a good method not to lose any more information :) ..and it seems like the story is not very recent, so there has to be some more to it..

Wise words...

Naturally Speaking

Naturally Speaking

I would like to share this blog by the Institute of Biodiversity, Animal Health and Comparative Medicine at the University of Glasgow and mostly edited by my cool supervisor Dr. Shaun Killen (NERC fellow interested in the physiology and behavioural ecology of marine and freshwater fishes, and also karaoke) :) :) I hope my research gets in there some day :) btw, I'm loving the idea of podcasts!! :) Great job to all!

Some of the Sightings @ the Isle of Mull

GREAT experience!!! :D

Plastic bottle fish sculptures on Botafogo beach

Plastic bottle fish sculptures on Botafogo beach

Harvest flies

This topic is a bit irrelevant, non-marine and non-phyloinformatics.. but climate change and temperatures issue is a maojor part of my dissertation topic... It's probably my first June I feel so cold, I even miss the sound of harvest flies... So I couldn't help but wonder...Have we seen any changes in harvest flies due to global warming?? After a quick research.. I couldn't find a decent paper and research on Tibicen canicularis. But I did run into this video again, reminding me that it's probably not the last June that I can't hear the Harvest flies sing (and not the grass hoppers as referred in the video.

Can Fish Remember???

MindGenius Mind Mapping Software

This is Genius!!! I wish I had explore that earlier... It looks like a really good software for brainstorming and capturing ideas and later presenting them. I will keep it for a further reference.. it looks like it will be very useful for my project. I could have been useful for my phylogenetic trees for my phyloinformatics project...oh well..when I use the free trial, I will add a comment on it..but other comments on the program are also accepted. :)

NCBI_Blast_Tree

The process of making a phylogenetic tree is simple in essence, however in our case, where we had to deal with many new species; to make a proper molecular tree would be a challenge. The basic steps involved in creating a tree from molecular sequence data are: (i) Some collection of sequences obtained from the NCBI database by a BLAST search and (carefully) aligned to put together homologous residues, nucleobases, or amino acids in case we want to compare proteins. (ii) Identifying other sequences that are related to the sequence of interest and obtain the data for that sequence is also a crucial step. (iii) Aligning the sequences and finding the differences between all pairs of sequences would be our next step, we would use ClustalX in order to accomplish that step. (iv) Using the alignment results, we can generate a phylogenetic tree. (source: "Phylogenetic Trees Made Easy - A How-To Manual for molecular Biologists" - Hall G. Barry) Our first step was to Refine our data table and find the NCBI codes for each specie.

Filtering our data for all the species that have a NCBI code.

As we can see, most of the species did not include a valid NCBI ID code, since they are still new species. Another reason could be because of a spelling mistake in their scientific name, are because the same specie could be know with another scientific name, causing a confusion. While filtering the data, we got only 100 species that contained NCBI ID number, out of 328 species in the list. And only 70 species had both NCBI and uBio ID names. I've decided then to look in NCBI Taxonomy database for a small group of new mammals and compare them and try to make a good molecular tree for this small group. Unfortunately it was very hard to find sequences of the same protein or molecule in each of the species and then make a sequence alignment with ClustalX. ..... The best tree I could manage to find is a typical tree in NCBI, where I used the NCBI codes that I had produced in Google Refined table. NCBI Tree

In our Data, only 169 species appeared with NCBI codes and these came out to our Taxonomy Tree in NCBI. Dominic and I tried to save the file in different available formats. Unfortunately, we do not know how to open this file after we save it. We tried using PHYLIP, since Dominic used that while attempting to make a tree, but it didn't work for some reason.

Errors...

I have downloaded and tried many of the programs I found in this page.. Even though I was hoping to work with TreeView and figure things out.. Treeview wasn't very friendly to me. I tried to follow the instructions given in the manual and while I was trying to make a taxon list and load it to the program, I would always get an error for some reason. I also tried to paste a nexus script example, but still wasn't working. I uninstalled the program and installed it back again...nothing. So, I gave up and looked for something else. Then I worked a bit with NDE, but I couldn't really understand what was it producing.

Ahhh... ok lets take it from the start. I am forgetting what I have done in the first place while I search stuff, get lost from one link to another, stick on errors and then can't remember where I began from. First step: BLASTING the Cricetidae family.. We're getting a good looking result, but it's not what we need..I feel lost, need to revise my course notes again.

Trees trees trees..

My friend Dominic has done a really good job on trying to create a KLM tree using Nexus, just like we learned in our Phyloinformatics course, our problem is that we should give our tree some dimensions in space. So I decided to play a little with the content of the data.. I chose to work with one family of species, the one that we have the most species on. so I filtered our table in order to show only the order Rodentia and the family of Cricetidae.

First I've tried to see if the iphylo Mashup could give me some information...but, unfortunately, no luck in getting a tree from TreeBase. so then I though...ok I'll look in NCBI: and found the Taxonomy ID: 9989 for Rodentia and then found the uBio classification of Rodentia but no further information about our new species. Blasting the ID code also gave me a tree, but I could not associate it with our data. Then I repeated the search in NCBI while doing a Cricetidae search. This time I think I got better results for the Taxonomy ID: 337677. and I can also download a csv file for that one. I will need to try and figure out how can I match those results into our "New mammal Data" and merge that into a nexus file to make a KLM 3D Google Earth tree. ...Interestingly enough, there are soooo many ways to create a phylogeny trees. HERE is a list of programs that can be used. I will experiment and try to make a tree by using TreeView.

Google refine

I've tried to refine the data and find the existing codes for each of the new species...The source I used is uBio FindIT - http://iphylo.org/~rpage/phyloinformatics/services/reconciliation_ubio.php, as suggested by our professor in our Phyloinformatics course. So I've updated the table that we are going to work with. Hopefully this will let us create a phylogenetic tree for some of the species. Unfortunately, the number of species without an ID code are still many: This pie chart shows the percentage of the new mammal species that are still without a unique ID: 57.9%. In our report we will analyze the importance of globally unique identifiers for species.

Data mining for our tree..

Dom and I, we have extracted all our information from our pdf paper into a csv file, however is seems like we're getting errors while following some steps... we're working on it...

...next step...google refining and working on the NEXUS code...

Google Earthing...

Dom and I, we created a KLM file and this is our result in Google Earth :) The red dots appearing in our map are representing our new mammal species since 1992 (source). They are not very clear in the video but, we can see that in certain areas (especially islands) there are many new species found. Once we have our data extracted..It is time to make a 3D Phylo-Tree!! :)

Hmmm...why hadn't I seen this option earlier?..

Testing if the graph's visuals work.. The graph is showing the number of new mammal species that were found in each order, since 1992. Aggregating by family:

More and more web pages and data...

I keep getting lost into new web pages...they all seem like they have loads of useful specie distribution related information, but I need so much time to look through them... I'll just bookmark them here for now and hopefully I will find the time to review the information until Friday.. NBN Gateway and BioMar