Saturday, 27 February 2016

Leatherback Turtle near Cairns

I get cheeky and go out to the Great Barrier Reef in my open boat on calm days.  Today, I was in deep dark blue waters about 5 km from the reef when I passed by a giant turtle basking just below the surface.  It did not seem to be worried by a 40 horsepower outboard passing by at full throttle only 20 m away.  However when I turned and can back for a closer look the turtle lifted its head up for a look, saw me and departed to the depths.  I don't think there was anything wrong with the turtle.
Leatherback Turtle near Green Island-Cairns North Queensland

The special thing is that there are no published records that I can find for leatherback turtles (Dermochelys coriacea) near Cairns.  The nearest record in the Atlas of Living Australia is from Mackay and dates from 1985.  Another record shows on the map near Cooktown, however this record is for a fossil!  Leatherback turtles are endangered, so this sighting is significant.

The water was clear and there were some small clumps of floating yellow-brown algae, probably sargassum and occasional lines of widely dispersed mangrove detritus.  However there were no major collections of floating materials which would indicate a downwelling zone and there was no other wildlife activity in the area.  In the water, transparent jellyfish with fine filaments at the edge of the bell were visible (Aurelia?) on the reef.  I even photographed one strange jellyfish then realized that the bell had been eaten by something, probably a turtle.  Leatherback turtles eat jellyfish as do green turtles.

Checkout the teeth a Leatherback has for dealing with jellyfish in this blog

Tuesday, 23 February 2016

Around the Rocks at Island Point – Port Douglas

Sometimes you can't get to the Great Barrier Reef because there is not enough time, the sea is too rough or you can't afford it. It is always good to know a few areas that are easy to get to and that can provide a little adventure.  Today, I walked around the sea coast of Island Point which is at the end of the famous Four Mile Beach at Port Douglas.
View from near near Port Dickson (click photos to enlarge)
View from near Four Mile Beach
This time instead of clambering over the cliffs at the Four Mile Beach side of the headland, I walked in from the Dickson Inlet side, which proved far easier.  On rounding the first corner, all of the bustle of the busy tourist port was left behind and it was like being on a deserted tropical island.  It is the kind of place Bear Grylls uses to challenge modern humans.  It was 37 degrees Celsius, and despite a sea breeze in the Port, the rocky coast was almost airless and 100% humid, right in the danger zone for the unacclimatised.  Visiting this area requires the crossing of almost a kilometre of large round boulders.  These boulders have a layer of ancient blue green bacteria (Nostoc) which is natures first attempt at a non-stick coating.  Finally, with the mangroves being close there is a low but credible risk of crocodiles, there are nasty oyster reefs and the rocky coast is where the toxic jellyfish breed so swimming around the headland is not recommended.  If you are are fit and take care then you will be rewarded with a rugged coastline featuring dozens of rock pools full of darting fish.
A rock pool with a black sea sausage
Juvenile diamond-scale mullet and two sergeant majors
Most of the fish present are specialised for living in rock pools and include a variety of gobies, pipefish, dart fish and juvenile reef fish which use rocky coasts as a nursery.  If it is high tide or if our seasonal 15-20 knot trade wind is pumping large waves onto the coast, very little of this marine life will be visible.

Higher up are smaller pools in the black rock.  These have grazing snails and sometimes even have live coral! It seems that under the right conditions, coral is even tougher than algae.  The rocks were so hot that the limpets were almost being cooked alive.

Most of the bottom of this tiny pool is covered by colony of hard coral.  It has a touch of bleaching on one edge.
Nerita costata snails feed on the thin layer of algae
Heat-stressed limpets were holding their shells as high as they could to cool down
The sub-tidal zone is dominated by brown macro-algae and black sea urchins (Diadema).  I do not know if this community is a recent community that has developed due to climate change and loss of coral.  Until recently it was incredibly hard to make an environmental record, there were no GPS, no cheap underwater cameras and each photo cost a dollar which is probably 1000 times the cost of a digital photo.  I only have fading memories of what places used to be like twenty years ago and these often do not include vital information such as which season it was.

The coast that I observed a few days ago is not that different to temperate coasts where algae dominate the swash zone.  Under the water, algae cover the rocks and a few metres further out the rocks give way to sand flats.  In this underwater rock garden, sea urchins are the gardeners.

Boulders quickly give way to a sandy seabed 
Diadema sea urchin
Close to then end of the headland, rainforest gives way to patches of natural grassland with pandanus trees due to the constant blasting of wind and salt spray. Up the top, parts of the hill belong to very rich people so avoid the temptation of bush bashing up the slope.  To get to the top, find the path at the end of the headland.

As with any posts on this blog, original photos and data are available to anyone doing biodiversity studies.

Monday, 15 February 2016

Introducing the Subject Index

Please start with the Subject Index if you are looking for something.  It is in the panel on the right of the page.

Humans still do a much better job of indexing books and websites than computers. So I have indexed all of the posts on this blog manually and the result is the subject index. Compared with search features that come with Blogger, an index made by a human is like a magic map of the blog that lets you find things instantly.

If you have a great blog where old posts are getting buried in archives, read on.

Making a back-of-book index

At first, I just tried to create an index directly as a word document.  This was very painful as it is very hard to be consistent and it is so much hard work to scan posts for items that should be indexed.  So I wrote a program to help me index the posts.  The type of index I created is called a back-of-book index and can only be made by people.

At first the program scans all of the posts and makes a list of words that it contains.  The list of words
is called a Concordance.  There are a lot of words that no one is interested in within the Concordance such as [the] or [a].  More than 95% of the words in the Concordance tell us nothing about the subject of a post.  These words just help make sentences.  The trick is to display only the 'subject' words and hide the rest.  So after each post is scanned, the program displays the new words it has found so that I can flag the subject words.

To create an index, I view each post and the list of subject words found in the post.  I cannot make an index directly from the subject words as there are many issues.  For example scientific names get broken up into two separate words when they should be treated as one word.  Most of the words in the list are also marginal to the main subject.  Putting too many words in an index creates information pollution.

This is the process for indexing a page using a program I wrote in ms-access which is a very easy place to write small programs.  It is good to have a switchboard which opens the forms you need in work flow order.

Next, I have to paste in text from the blog (see below). The post that I am indexing is the one on Popeye Mullet.   One day I will automate this step.

Then I scan for new words and flag the words that have subject relevance.

Next, I scan the new post for subject words.  The list is not bad but there are many words that are peripheral to the subject of the post.

I type the items I want in the index into the box below.  A category can be added in front of any item by using a back slash.  I have also decided that common names will be followed by scientific names and that scientific names will not be followed by common names.  Making cross-references like this is a key skill of human indexers.

Next I generate the index for all posts as a table and there I can edit entries to make the formatting more consistent and to add information that points to the differences between similar posts.  The edits are saved so I only have to make them once.

Finally I preview the index in a browser.  Here I can see errors such as the fiddler crab entry being displayed without a category.

It is quite easy to generate html from a database table.  Here is the actual code that generates the code for the index from the database table.

The code above makes the html text, which is then placed in a text box so I can just copy and paste  into blogger to create the site index. Clicking on the label beside the text box selects the text, then I press Ctrl-C to copy it (including all the lines that do not fit in the box).

I wrote my own indexing program because I could not find any on the net other than old programs that no longer work or very expensive professional programs.  The entire program took about 8 hours to develop.  In its current form the program is basic but it works.  Let me know if you are interested.