marine biology

So… ever since I first realised what marine biology encompassed (1st year science I guess) I have been a fan. I already had my mind set, I would be a virologist. Nevertheless marine biology entrigued me. I enjoyed subjects like ecology and animal biology during undergrad and did well in them. During my PhD I tutored on the side at UQ’s Moreton Bay Research Station. The things we covered were mainly for advanceed high school students interested in ecology adn marine biology – but it was still damn fun. Walking across “rocky shores” looking at the wildlife. Examining the life amongst the mangroves. Snorkelling in the murky disgusting water of Moreton Bay’s reefs. I got to do cool stuff like play with exotic fish, feed sharks, pick up a wobegong, pick up Sting Rays, catch crabs, play with octopus and swim with dugongs. I loved it. I liked it more than simply because it was a break from molecular virology/biology.

Now I play with cells all day long. Yeah I still play with viruses and examine the innate immune system, but for the most part it is cell biology. I love cell biology, examining the intricacies of cells. For the most part it is fun, with expensive toys.

My recent trip to Port Douglas, and snorkelling on the reef – reminded me of how much i love Marine Biology though. It’s fun. They are real. So much is unknown about the creatures that navigate the seas.

I have been watching some hardcore HD videos c/o iinet’s Freezone (Earth Touch http://www.earth-touch.com/ ). It inspired me to post some pics of the Agincourt Reef, outer Reef, Great Barrier Reef that I went to with Quicksilver Cruises.

Here’s where Agrincourt is.

Anyway. A random selection of the photos are attached. Of course these are all copyrighted to me, aaron irving. Steal and die.

Most of these shots are from inside a semi-submerisble. SHot threw a thick glass window, no flash, iso 250 or something.

A Holiday (pics included)

So – it has been about 2 1/2 years since I have had a holiday. Yeah I have gone away for a long weekend, taking 2 fri/monday off work. That was living it up. Now I am currently on a 2 week holiday. It feels weird.

Due to poor organisation, our original plan to visit thailand was cancelled. Just as well – the political riots and 20+deaths (3 western tourists and 3 journalists included) makes it less than ideal to visit at the moment. Not to mention the early rain season.

Regardless – we booked a quick trip up to Port Douglas

 ,

flying in to Cairns and then driving and staying @ Sea Temple

  .

Of course Steph hadn’t been to the great barrier reef – so we jumped on a boat

and went out to Agrincourt on the outer Reef

.

Steph even went in the water

 

with the crazy fishies for some snorkelling and we also went on the semi-submersible

.

Apart from the pretty coloured fish, there were pretty coloured coral and turtles

.

We went for a drive up Kuranda way to see some forest

and stopped at Palm Cove on the way back

  .

The rest of the trip was mainly relaxing ,

drinking wine   and

watching the sunset .

ipad, pricing and indecision

Hmm. Well the apple australia pricing has been released now. he indecision kicks in. Is it worth it compared to windows tablets? What options etc.

The pricing.

WiFi: 16Gb $629, 32Gb $759, 64Gb $879

WiFi + 3G (+GPS): 16Gb $799, 32Gb $928, 64Gb $1049

You can pre-order from Monday. Delivery, end of the month.

v persie

So – I don’t normally support arsenal, I still didn’t go for them, I do however feels sorry for them. Tottenham played really well and deserved the win. In case you haven’t guessed I finally had time to watch the replay of arsenal v tottenham. The spurrs did awesome to keep themselves in the running for 4th place. While I want man city to get it – good on them.

Now – the game did show the re-emergence of Van Persie. Damn that guy is good. If Arsenal had him the whole season surely the top of the table would be different. I think he would have also given drogba and rooney a run for their money (as lead goal scorers in the premier league).

Anyway I was going to say more but I can’t be assed. 30 minutes Man city takes on Man Utd. – I hope man city kicks their ass and takes 4th place (giving chelsea the title). A bit of a change for a player that normally supports man utd. What can I say – I am aussie and support the underdog.

ipad, slate random photos and whatever else I want to add

Anyone who knows me knows that I like technology and gadgets. Especially touch screen like my modified, hacked gps or smartphone. The ipad has a lot of potential for me – as a pdf reader and note-taker during meetings/seminars. Great for travelling. There are some serious software limitations (forced to use itunes store, no flash for websites etc). It is good hardware though, with an impressive battery life.  I did a fair bit of research on tablet devices recently, like the netbook navigator, viliv, archos, mini, notion ink, wepad, evo. I also went straight to the manufacturers in china to see what was coming out. While some have awesome specs – they have crap battery life – or vice versa. I had basically given up on a decent windows or android alternative – then Hp releases specs and a demo on the HP slate http://bit.ly/amG5u6 . The battery life is looking like 5 hrs but more powerful then the ipad, running full windows 7 with multi-touch, flash, hdmi out for monitors/tvs – usb ports for hard drives cd’s etc without paying crazy fees for a mac adaptor. Expected release date is june. I think I might just have to wait for it now, despite basically deciding on buying a 3g ipad when it came out.

I was going to ramble some more about sitting on a microscope for 7hrs today (either taking images or battling with linux – Cent-OS sucks, as does applied precision for picking it), or how it sucks when you are working days and she is on nights.

Here are some random pics – you should try and guess the relevance.

US army killing civillians, media and visas

So, some topics people post online end up being listed by the US gov’t and can potentially impact visa applications etc. I know of several examples where it has happened recently. C’est la vie.

This footage  http://bit.ly/9V5NBP was recently brought to my attention by Josh (author of a beginners guide to dying in India). It is one of the more fucked up things I have seen. Yeah there are two guys carrying rifles – but they are crossing the road and not engaged in any sort of activity. 11 people died, 2 children, 2 journalists. One of the journalists was a 22yo iraqi war photographer whose work I had seen on deviantart. Both journo’s worked for reuters. At one point his canon l series lens is regarded as an RPG from the US troops in an apache helicopter above them. He died soon after. The US troops also laugh after they discover they shot 2 children saying “they shouldn’t have bought their kids to war”. Pity that the parents were just picking up wounded friends in a van.

The messed up things about this – it is now over 2 years since the event occurred and wikileaks released the story. Apart from that I recently found out that a Saudi Arabian friend had this footage close to two years ago… and it was released in islamic media sites but just never made it to main stream media. Civillians die in war, but these guys are ridiculously trigger happy and show no remorse for killing civilians. They need to learn the value of human life.

GPS satnav maps: whereis vs navteq

So as most of you know – I like to have an up-to-date satellite navigation system. I run a chinese no-name GPS unit (with dual processor, wince5, word, acrobat, mp4 player etc and built in tv tuner). I also have it on my HTC touch diamond 2 phone. The software I prefer is igo (Igo My Way 8 by nav’n’go). It does the usual tricks with points of interests (POIs), built-in speed cams, speedlimits. lane info, text-to-speech (TTS) etc etc. The most annoying thing compared to garmin etc is the TTS does not haev an australian TTS voice, but the software is the most advanced and customiseable. Recently the maps have sucked and it has been very hard to get an up date. I was running the telstra 2008 maps then a december 2008 navteq map. There has been a constant battle between the two companies: sensis- whereis (Telstra) and Navteq (Nokia). Whereis was the gold standard for years and navteq sucked. Then navteq made a comeback in early 2008 with brilliant maps. Not quite as good for inner cities etc but great for rural/ parks and the like. Anyway there was a long delay with getting a new map update but now the R17 whereis (jan 2010) map is out and I have started using whereis again. I have to say I am impressed. So far the maps are accurate (in melbourne), lots more POI information, lane info, speed limits, traffic signs, school zones (that only show up during school hours). The maps aren’t perfect and a few speedlimits are wrong already but most of the new highway info is alrady built-in. I am sure navteq is still better for in the outback but I think whereis might finally be making a comeback (companies like navman and mio swapped from whereis to navteq as whereis was too slow in updating). I will wait till I get my hands on the new navteq maps though to make a true comparison. At least I won’t haev to change software just to get a new map now (yay) as I was starting to play with Navigon mobile navigator just so I could have a 2009 map working.

“Young” professors and 300,000 at RG

I got an email today from scopus with the awards for the “young” scientist awards in Aus. It’s pretty fun that most of these young researchers are already professors… I mean wtf. Maybe recognise some actually young scientists for once.

“Blah” The winners and finalists for the Scopus Young Researcher of the Year Awards are:

Award Category Result Name Affiliation Humanities and Social Sciences Winner Professor Peter E.D. Love Curtin University of Technology Finalist Dr Kylie Hesketh Deakin University Finalist Associate Professor Jennifer L. Hudson Macquarie University Physical Sciences Winner Professor Benjamin J. Eggleton The University of Sydney Finalist Professor Tanya Monro The University of Adelaide Finalist Professor Andrew White The University of Queensland Engineering and Technology Winner Associate Professor Dan Li Monash University Finalist Professor Rajkumar Buyya The University of Melbourne Finalist Associate Professor Lianzhou Wang The University of Queensland Medicine and Medical Sciences Winner Professor Prashanthan Sanders The University of Adelaide Finalist Dr Stephen Turner The University of Melbourne Finalist Professor Louisa Degenhardt The University of New South Wales Life Sciences and Biological Sciences Winner Professor Corey J. A. Bradshaw The University of Adelaide Finalist Dr Joern Fischer The Australian National University Finalist Associate Professor Frank Grützner The University of Adelaide For more information, please email Meiling at m.tang@elsevier.com

 

Anyway,

P.S. 300,000 members at ResearchGate now:

Everton! and the epl!

Well what can I say – well done everton. Chelsea has been a bit of a juggernaut this year and congrats to everton for a solid win over them. Louis Saha is an amazing finisher. Cahill did his usual solid job but no goals – ahh well. Baines is essential to the team and welcome to the English Premiere League Landon Donovan – he has fitted in well to Everton and the EPL. Anyway they did well. and made the fight for the winner more interesting for the Chelsea/Man UTD battle. Everton should have been playing like that all year.

Man city has done alright – winning matches though not looking top confident. Definitely good to see them into the champions league (most likely anyway).

Wayne Rooney is a damn good player but a draw was all they deserved. Arsenal certainly aren’t the best team this year (sorry daz) but they are better than liverpool. so yeah – that’s fitting anyway. Liverpool without Torres just isn’t right.

Will be an interesting finish to the year and a good welcome to the world cup in South Africa…. speaking of sporting events – did you see the photos in the paper of the indian children shovelling dirt at the commonwealth games sites?. Seriously sad photos – but awesome journalism. New Dehli will really struggle to finish the venues on time for the games – so good luck to them!

On another sports note we are back to indoor net week. Go Monash UTD or whatever the hell we are called this year.I need to get my ass into gear for the victorian universities cup – since I am organising it.

Anyone want to sponsor us? The financial crisis sucks in that regard.

thoughts on the ipad

Despite it’s nicknames such as the itampon – it poses an interesting idea.

So we all know by now it is basically an iphone on roids.. – so what’s the deal. The deal is apple. They are a marketing power not to be taken lightly. They do a damn good job of convincing you that you need to buy a shiny version of relatively normal hardware. So…

Software: Basically if you have used an iphone you will know how to use the ipad. Why they didn’t choose a lighter version of OS X – who knows. My gripes – single program usage. In today’s world, people are use to multi-tasking. They have multiple programs at once. Like the iphone the ipad only lets you have a single piece of software running at once. There is no minimise, its open or close. This is a smart idea as it minimise the need for large amounts of RAM (of which apple doesn’t say how much in the Tech Specs.  It’s also annoying as all software must be loaded via itunes – no plug and play. At least until you hack it and therefore void your warranty. Of course this forces you to use apple software, have an apple account – list your credit card details in the apple store and yeah – be one with apple. I am surprised that the US government hasn’t deemed this some sort of anti-trust, c’est la vie. The 3g model is the only one I would consider – this also gives you a choice of GPS software – if you feel so inclined. Several features such as ibooks aren’t available in australia (and won’t be for at least a year, if ever). This is due to licensing agreements with the authors publishers.

Hardware: Now this is nothing new. It’s all been around before. Apple claims they have this special A4 processor that is all theres. It’s based upon the typical ARM-based processors found in your GPS or smartphone and made typically by centrality or samsung etc. They are good processors and power windows CE, windows mobile, android, win 95 (on a nokia) or even linux (tomtom etc). APple has modified – and supposedly produce it themselves (which is a first in a while). This version runs a 1ghz chip – which is pretty damn fast for a little device that only runs one program at a time. I have a more powerful than average GPS unit running a dual-core 600mhz ARM chip and it is damn impressive what it can run (my GPS plays divx’s, has a DVB-T tuner in it, opens word files, opens pdfs, has corel draw, reads out ebooks using text-to-speech etc). These ipads come with various size flash disks (!6, 32 or 64gb) which is nice. Of course they are tablet-only (multi-touchscreen) which is getting more and more common – and the way of the future. All will be that way soon enough. It is a 9.7” screen (diagonally, non-widescreen). Why the hell aren’t they widescreen apple – they would be perfect for playing movies. They also only run 1024x768, so despite having a good quality, shiny, pretty screen, isn’t even true High-Definition.

I guess apple is the first to put it all together with a 10” version – but the 13” netbooks are getting damn common nowadays (and make a lot more sense for travelling than a laptop). a 10” tablet will be available by other manufacturers soon enough (one would imagine). The other features like 3g, N(108mbps) Wifi, A-GPS, acceleromator, light sensor, etc are all found in current ARM-based GPS devices with touchscreen (though not many on the Australian market – I can get all of those features on a 5”/7” iphone clone GPS device for about $200/$280AU incl. duties). The apple software does multi-touch better than most though and they are the first to do it in 10”. It is interesting to see how well it goes. It looks damn hot and the apple marketing will tell you need it (especially to go with your iphone or apple mac laptop). For me the ability to only run one piece of software at a time and forced to use itunes is a deal-breaker. It’s a big NO from me…. though it looks sexy and I don’t have one.

The demise of coffee in Melbourne

As most of you know – Melbourne has some damn good coffee. It has some crap coffee and a lot of average coffee, but yes, some damn good coffee. The problem is – you find a good place and then some toss* like Matt Preston writes a review and voila – busy as hell. Two of my favourite places have slowly declined in quality that much that I don’t even want to go there anymore.

Liar Liar in hawthorn, just hasn’t been the same since the owner sold it and moved on. The new staff just can’t cut it and I have actually had bad coffees from there. The vibe is just all wrong aswell.

Chimmy’s in Richmond – again just can’t cut it with the crowds lately. Cold meals, massive waits and then the coffee is more often average than not lately. Very disappointing based on how good it has been in the past. They have all their fresh-baked goodness though.

A lot of places are just dishing out mediocre coffees as they can’t handle the amount of people anymore… I blame the write-ups for all the extra people. It certainly can’t be the global financial crisis.

Anyway there is hope. The dancing Goat in the city. St Ali in sth Melbourne. Artichoke and Whitebait @ Monash. Jones @ Chadstone. Ilios at Richmond. The new merlo place in degraves. Di Bella in nth melbourne or at the vic markets. The green room @ Brunwsick. BBB also in the city and lat but not least, BBB’s sister – Seven Seeds at Carlton. There are plenty of other Gems around but Seven seeds takes the cake.

Definitely my pick of the cafes in melbourne at the moment.

One day soon I will do up a list of all the good cafes/coffee places to visit.

Avatar, heat, work and molecular therapy

I am kind of fond of long random titles for blog posts.

Just got back from seeing Avatar in 3D with a good mate who is visiting from Tasmania (Seth). James cameron did a good job in re-creating a fantasy world, as did Weta Digital. I quite liked the storyline and character development – despite the bad reviews. Was a visually stunning movie, though I felt a little dizzy/headachy by the end. This was likely due to the heat though and my dehydration. 36 degrees is not that hot (when not humid) – but the warm wind makes it pretty uncomfortable.

More warm weather to come – yay. Christmas in Brissy though so the weather will be nice then. A whirlwind 4 day trip, but c’est la vie.

Work has been busy. Yay. As per the monash guidelines we have from the 23rd to 4th jan off. I was in today though to do a maxi – got a cool new construct in that I want to use asap. Writing up my paper (actually several') – hopefully a decent impact factor first author though. Got news today the Molecular Therapy paper with Michael got accepted (I’m an author anyway, even if not first). Papers are always good. Finally on top of things and starting to feel comfortable. Eventually I will get motivation back and maybe even be inspired to go out photographing. meh, maybe.

Enjoy the break peeps – happy festivus (As daz would say), merry christmas (remember it’s about jesus and not gifts/food) and happy new Year!

oh the pretty lights

So recently I went to a conference on lights. Pretty lights. Fluorescence if you will. Lights in Life Sciences 2009. Damn impressive. What people are visualising with ocnfocal microscopes, widefield microscopes, 3d structured illumination, PALM, dSTORM, STED microscopy etc. Being able to visualise single proteins within a cell via a tagged fluorophore. It’s impressive. Kudos to the people coming up with the new technology – and to those developing the new fluorophores (a  lot of these techniques require photo-switchable fluorophores such as dendra, eos, PS-CFP2, kindling etc). I can easily see why the big journals are asking for this sort of technology rather than basic microscopy and “colocalisation”. I am glad to have a project that has allowed me to develop skills in advanced confocal microscopy.

I think I want to learn every available technique and then consult out.

I also covered my poster at the conference and a second poster for the ever evolving http://Researchgate.net

hmm. back to work I guess.

p.s. clannzu sounds damn good with rain in the background.

argh

So. another rant. I kind of remind myself of Foamy sometimes - http://www.illwillpress.com/vault.html 

Anyway, I felt some serious road rage today. If it wasn’t an overloaded ute seriously driving 30km/hr down the freeway it was a bag of clothes falling off a truck onto my windscreen or a cab cutting me off by driving up a traffic island and almost toppling over (the cabbie even looked scared and grabbed his window).

Ahh melbourne – some crazy roads. The weather here is great though – a bit of heat and very little humidity (so far anyway) unlike what I have heard brissy is like.

Seriously almost snapped and killed a crazy driver today – well not really.

6 1/2 hrs of continuous confocal (FRAP) – yay what a good day.

so anyway…. Neville Parish will soon make a debut at http://www.cityonahill.com.au

Leonardo’s Last Supper

Awesome.

The piece, by Peter Greenaway, is pretty impressive. A unique mix of artwork, lighting, music and pojector/cinematography. Short (20mins) but sweet. I found the use of lighting/projector on top of a fixed painted image to be a pretty decent blend of skills. If you are in Melbourne – it is going on for another 2 weeks. http://www.melbournefestival.com.au/program/production?id=3505 Check it out.

visually disturbing

A few visual sights I have found disturbing recently:

- A 5yo girl wearing a miniskirt so short I saw her g string when she bent over.

- A pink toilet bowl on the side of the street that someone had taken the initiative to use (hard rubbish collection, where people dump furniture etc on the side of the road).

- Someone had stuck a photo of a guy on the cow up a tree - http://blog.panedia.com/2007/04/27/docklands-cow-up-a-tree/

-clayton

-One of the regulars at my local pub spill bill on himself because he was trying to drink while pissing at the urinal.

- An indian cabby getting changed in the back of his cab (fully changed).

-The amount of blood that can be mixed with snot when you have a seriously blocked nose.

-The fungus growing on one of my supposedly ‘bacterial’ plates.

- The ants pouring out of the mini-CBD buildings in the docklands and running to get to the train station (by ants I mean people in suits).

Rio beats Tingalpa for the 2016 olympics

South America is celebrating as Rio De Janeiro wins it’s bid for the 2016 olympic games. This bid would normally be worth celebrating – however they only win over the unsuccessful bid of Tingalpa. Tingalpa, a small suburb in Brisbane, has now failed for 3 olympic bids in a row. More information about TINCOG’s bid can be found here http://tincog.splunge.net.au/

Science is cool – See the Bloodlamp

 

So – science is geeky. We all know it and embrace it. Sometimes you can use geeky scientific knowledge to make cool objects.

The bloodlamp by Dutch designer Mike Thompson is a glass ball filled with Luminol. It reacts upon binding blood to fluoresce – hence giving off light.

Pic c/o the NS pic of the day - http://www.newscientist.com/gallery/dn15018-pick-of-the-pictures

It was designed to make the person think about how precious energy is and how much they really need light.

anyway – how’s that for a random post of the day.

Important questions to ponder

Why must one walk up a rampfrom the footpath to get to “lower ground” in my complex?

Why was there one supra, one mitsu Evo X, one GTI, one skyline GTR, 2 HSV coupes a WRX STi, a civc type R (rally prepped) and 2 highly modified nissan patrols in my apartment carpark at midday? Why spend lots of money on a car then leave it parked in the garage all week long.

Why does the name “Craven Cottage” sound so cool?

Why did the butcher let me down? (Worst lamb shanks ever for diner tonight, I swear the sheep must have been 20 yr old reject stock).

Merlo or Di Bella?

Why does the microscope work fine when your cells don’t express the protein properly, but screws up when you get good clean expression?

Enough questions for now anyway…..

On another note, I’m going to cross post my ResearchGate Blog posts from their to hear aswell. Starting with this one on Gene therapy to restore color blindness.

A recent Nature letters paper by Mancuso et al details the use of a recombinant adeno-associated virus (rAAV) in gene delivery to restore the function of photo-pigments in squirrel monkeys. The male monkeys, red-green color-blind from birth, obtained the ability to process red-green color information via the delivery of the L-opsin gene into the retina. 

While this research opens the door for further hope of gene therapy involved in human eye conditions, including blindness, it also raises some interesting questions. It was previously thought that the brain of adult monkeys would be too "hard-wired" to gain a beneficial effect from the restoration of deficient pathways. The recent paper proves that gene therapy can be utilized in "middle aged" monkeys, and is not solely an avenue to be pursued during early development. This adds a lot of significance to work already begun in human patients, to restore an enzyme involved in a type of hereditary blindness.

Original Article:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08401.html

Gene therapy for red–green colour blindness in adult primates

Katherine Mancuso¹, William W. Hauswirth², Qiuhong Li², Thomas B. Connor³, James A. Kuchenbecker¹, Matthew C. Mauck³, Jay Neitz¹ & Maureen Neitz¹

ResearchGate providing free access to journals.

This is a pretty awesome loophole potentially allowing free access to journals people would not normally have available.

ResearchGATE launches SelfArchiving
Repository
Scientific Online Network ResearchGATE blazes a new route into the world of Open
Access
Boston, September 15th 2009. The last few weeks have been big here at ResearchGATE
(www.researchgate.net), the world's largest online scientific platform. We have only been online
since May last year, but already have 140,000 members. Recently, we introduced our
international Job Board for Science and Higher Education. But today is set to be even bigger, as
we are launching our SelfArchiving
Repository. This will make full‐text articles available to the
public, for free – the first application of its kind worldwide!
Currently, there is no way for researchers to access millions of publications in their full version
online. ResearchGATE is now changing this by enabling users to upload their published research
directly to their profile pages (a system called the “green route” to Open Access). Our
publication index, containing metadata for 35 million publications, will be automatically
matched with the SHERPA RoMEO (http://www.sherpa.ac.uk/romeo) data set of journal and
publisher’s selfarchiving
agreements. As a result, authors will know which versions of their
articles they can legally upload. Since nine out of ten journals allow selfarchiving,
this project
could give thousands of researchers immediate access to articles that are not yet freely available.
Our SelfArchiving
Repository does not infringe on copyrights because each profile page within
ResearchGATE is legally considered the personal website of the user (and the majority of journal
publishers allow articles to be openly accessible on personal homepages). Therefore, each user
can upload his or her published articles in compliance with selfarchiving
regulations . Our
publication index makes every publication identifiable and is searchable. Since each profile is
networked to the larger platform, the uploaded resources will form an enormous pool of
research for our members. Of course, it’s free of charge, like the all the other resources at
ResearchGATE.
To learn more about ResearchGATE and its many features, visit www.researchgate.net and sign
up for a free profile. Also, feel free to contact our team at press@researchgate.net.
To learn more about SelfArchiving,
visit www.self‐archiving.me