An idea that not altogether weird. The question should be considered.

February 8, 2012

We tend to see extinction as a bad thing, particularly a native species in its native habitat. If you don’t think human caused extinction is a bad thing – perhaps you should reconsider.

So what if the species going extinct is ‘not a nice’ species, and what if we are making it extinct deliberately? The question has been asked regarding smallpox virus which now exists only in the preservation freezers one or two highly secure labs. People who understand the complexity of the web of life and the importance of complex ecosystems as critical to human survival  do see this as a serious question.

One website – considered satirical by some – is dedicated  to saving the Guinea worm, Dracunculus medinensis a human parasite that to the uninitiated seems a bit unpleasant. Should we deliberately make extinct species such as this? Is there a difference between genocide of a virus and a multicellular organism? Who should be considering the question? Should we call it gene-icide, nucleotide-icide or just speciecide? Or should the decision just be left in the hands of the missionaries, healthcare workers and locals who suffer the consequences of the particular parasite or pest or inconvenience?

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Fluorescence in Psedoscorpions?

January 5, 2012

I noticed the pseudoscorpion was glowing fluorescent under uv light. I was sure fluorescence had never been recorded in pseudoscorpions before, unlike real scorpions which are widely known to fluoresce. Although as yet there is little supporting evidence for any of the postulated evolutionary reasons for the fluorescence, which is widely believed to be due to the molecule 4-methyl-7-hydroxycoumarin (Frost et al) as the cross linkages in the hardening exoskeleton form.

Initially I was excited by the prospect of describing something new to science in this domain but a couple of things got me wondering. Why did it fluoresce only on the underside, why was it motionless and why didn’t I notice this earlier – was this because I had failed to notice the underside?

The following day the pseudoscorpion was still motionless, I was now inclined to think it was dead. It was, but sure enough it still fluoresced on the underside. I was determined to find out why, but these little pseudoscorpions were not that easy to find. I had only ever found one group of this particular species in the past in Eucalyptus leaf litter.

I crushed the dead pseudoscorpion in sterile water and did a streak on nutrient agar plates. Sure enough, over night bacterial colonies appeared that exhibit strong fluorescence in the same colour as observed in the pseudoscorpion. Presumably a Pseudomonas of some sort as it had the distinctive Pseudomonas odor.

So it seems I had not recorded the first observation of fluorescence in Pseudoscorpions, just a death by a fluorescent pathogen.

Leech Eats a Water snail

April 10, 2011

This leech was hanging around the pond attached to a new water lily. I put it in the petri dish to have a look under the scope – left a small snail in the dish too. Needless to say the leech emptied the contents of the snail shell over half an hour or so. In 15 minutes its intestines darkened and you could see the food through its translucent body. A few photos are more revealing. It is about 11mm long.

The Tiny Frog

March 30, 2011

Its been a great season for frogs this 10/11 spring and summer. The creeks are up, insects everywhere and spawning as if there is no tomorrow. Guess they are making up for the years of drought we have had to wait out.

This little fellow was in a creek which was running much higher than usual. In among the sharp grasses.

Day One

Day 2

 

 

 

 

 

 

 

 

 

 

Day 3

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Before metamorphosis the tadpoles were un remarkable.

Before and after

A Copperhead (Austrelaps ramsayi)

March 27, 2011

This one was killed on the road at 35°36’44.58″S 149°33’6.16″E on the Captains Flat to Braidwood road on 26 march 2011. Probably dead for a day or so.

Not sure how widespread they are in the district – NSW DEC Atlas of wildlife http://wildlifeatlas.nationalparks.nsw.gov.au/wildlifeatlas/watlas.jsp seems to be broken today.

Should be a good year for them now and next given that there are a lot of frogs around after the good rain. You can see a distinct vertebral stripe clearly in this one which was about a metre long.

Australeps ramsayi

Austrelaps ramsayi

A Brown Snake, Pseudonaja textilis – notes on a post mortem examination

November 27, 2010

She was just trying to cross the road when the ute in front of us ran her over. Writhing in pain  her crushed lungs meant she had no chance of survival. My first thought was a DNA sample so we collected her (just alive ) and continued on our way home. She was DoA. She was 122mm from snout to tail and weighed 404 grams. She had 17 scales around her mid body. Her scales were nice but she had three black ticks and a couple of lumpy scars – presumably from previous ticks. Orange dots peppered her ventral side.  Her anal scale was divided and her post anal sub caudal scales were paired. She was a lovely brown but had subtle stripes around her body which were most noticeable in the mid section. She had a nice svelte line but with a bump of a previous meal. Lizards I expect.

I dissected her from vent to chin exposing her vital organs. There was a significant amount of fat in the anterior abdominal cavity – clearly spring had been good so far. It was in NSW east of Canberra, east of Carwoola  (35°28’56.02″S149°26’40.55″E ) on 20 November 2010.

There were nine eggs in total.  Each was about 26mm in length but there were no signs of development in the egg contents which we a yellowish thick liquid. Lungs were mush from the encounter with the vehicle tyres. Her gut contained a 180mm blue tongue lizard, and a smaller skink complete with its tail. Interestingly there were several shed tails, 3 more than actual skink bodies found. Perhaps she was happy to eat the tail dropped in haste although they do not seem to be substantial enough to be worth much as a food source. Another possibility is that the tails were somewhat harder to digest than the bodies themselves, perhaps even because the venom had not circulated into the tail before being dropped. The venom aids digestion inside the prey animal and starts getting to work breaking down the prey animals body immediately on injection.

I sampled the tip of her tail, her heart and a couple of eggs in 80% ethanol for someone who may wish to compare DNA as an investigation of the geographic distribution of clades in the species. I guess I will send the material, and the ticks, to Rick Shine’s lab at University of Sydney, or the Australian Museum, where there is probably the best chance of connecting the sample with someone who is interested making use of it – now or in the future.

Eastern Brown Snake Pseudonaja textilis


Acetone Yoghurt

November 3, 2010

My favourite breakfast had a bit of spritz about it but it wasn’t out of date. I like my passionfruit yoghurt but did wonder why it seemed a bit lively and tangy this one morning. The following day I was crook with a cold which lingered and so did not have my ‘normal’ breakfast for a week or so. But then, when I cranked out the large tub of favourite yoghurt (still not past it’s use by date) I was overpowered by the acetone smell that emerged. The concentration must have been high as it smelt stronger even than a close up whiff of nail polish remover.

I read a bit online about bacteriological produced acetone. Clostridium acetobutylicum, the most well documented, is sometimes called the “Weizmann Organism”, after Chaim Weizmann, who in 1916 helped discover how C. acetobutylicum culture could be used to produce acetone, butanol, and ethanol from starch using the ‘Acetone Butanol Ethanol process’.

Still this organism seemed a little unlikely in this case as it produces acetone et al in anaerobic conditions, and a tub of yoghurt in the fridge at 4 degrees C didn’t seem like the ideal conditions for acetone production. I froze a sample on the off chance it might be useful later and streaked the yoghurt on nutrient agar in an effort to isolate the relevant organism. Clearly I will have to isolate it from the Lactobacillus and Streptococcus species I expect to find in the yoghurt. I wonder if this is a well known bacteria? I will update if I can identify it.

Fluorescence in Psedoscorpions?

October 30, 2010

I noticed the pseudoscorpion was glowing fluorescent under uv light.

Pseudoscorpion fluorescing

Pseudoscorpion fluorescing

I was sure fluorescence had never been recorded in pseudoscorpions before, unlike real scorpions which are widely known to fluoresce. Although as yet there is little supporting evidence for any of the postulated evolutionary reasons for the fluorescence, which is widely believed to be due to the molecule 4-methyl-7-hydroxycoumarin (Frost et al) as the cross linkages in the hardening exoskeleton form.

Initially I was excited by the prospect of describing something new to science in this domain but a couple of things got me wondering. Why did it fluoresce only on the underside, why was it motionless and why didn’t I notice this earlier – was this because I had failed to notice the underside?

Pseudoscorpions

Pseudoscorpions

The following day the pseudoscorpion was still motionless, I was now inclined to think it was dead. It was, but sure enough it still fluoresced on the underside. I was determined to find out why, but these little pseudoscorpions were not that easy to find. I had only ever found one group of this particular species in the past in Eucalyptus leaf litter.

I crushed the dead pseudoscorpion in sterile water and did a streak on nutrient agar plates. Sure enough, over night bacterial colonies appeared that exhibit strong fluorescence in the same colour as observed in the pseudoscorpion. Presumably a Pseudomonas of some sort as it had the distinctive Pseudomonas odor.

fluorescent bacteria

Strong fluorescence on nutrient agar.

 

Updates to follow as I identify the organism.

 

fluorescent bacteria

fluorescent bacteria plated on nutrient agar

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Frost, L.M., D.R. Butler, D. O’Dell & V. Fet. 2001.  A coumarin as a fluorescent compound in scorpion cuticle. Pp. 365–368. In Scorpions 2001: in Memoriam, Gary A. Polis. (V. Fet & P.A.Seldon, eds.).  British Arachnological Society, Burnham Beeches, Buckinghamshire, UK.

Contrails

December 22, 2009
Contrails

They remain long after the plane has gone

Some will call me pedantic but it really irks me that no matter where one goes – the sky is unlikely to be unpolluted by contrails on any given day. Recently in the Sturt National Park but also in the Simpson Desert and so-called East coast ‘wilderness’ in Australia the sky is visually polluted by contrails from passing aircraft.

One can also see this phenomena on documentaries – often from some far-flung place – where the background sky is littered with contrails. The BBC Oceans HD series which is a nice production is a case in point. The Atlantic episode off the Caribbean had – perhaps unsurprisingly – numerous contrails in the background.

Adding to the irritation is the idea of all those people sitting there drinking champagne and eating smoked salmon, and greenhouse gases pouring into the atmosphere at a rapid rate after slogging away to arrive on foot at some hot, remote or desolate place where one of the pleasures is the isolation and not feeling depressed at the burgeoning population for a time.

I wonder what today’s world would be like if flight had not been realized?

Of course I should probably add that I don’t support the bizarre conjecture that some contrails are a Government conspiracy of some sort. Nor are they a sign of anything.

Signs

December 21, 2009

I recently saw the movie Avatar (possible minor spoiler below) – which is a stunning piece of work by the way – but was struck by the ‘sign’ that the main characters observed. In particular the fact that it probably actually qualified as a ‘sign’ unlike than the rather droll matters that human have for centuries been alleging ‘it was a sign’.

The jellyfish-like Seeds of the Sacred Tree land on Jake’s outstretched arms.

A sign - from Avatar

Meteors, tsunamis, volcanoes and comets clearly don’t make the cut as a sign because it is obvious to all who care to look that they are solar system or planetary geological forces at work – any coincidence with a human activity is just that – a coincidence.

Other things that have been labelled signs over the centuries – a face observed in a cloud or rock, a coincidence of weather and some significant time in some human’s life – a funeral and a storm, a birth and a clap of thunder or an unjust death and a subsequent drought are just fanciful connections made by an over-active human brain. Of course the brain is acutely tuned to detect faces and some real processing power is given over to the task allowing the person to interact in a social community appropriately. A dog would do it differently. Similarly, evolving on the savannah, there was a benefit in drawing conclusions between things (wandering away from the troop and getting attacked by a lion, eating a new berry and later feeling sick) to aid learning and so the survival of the individual bearing the ability to draw rational conclusions. Unfortunately – as yet – there seems to be no commensurate significant selective advantage in generally avoiding making an inappropriate association between events. This is a sort of ‘err on the side of learning’ rule of thumb which must have served humans well in some way in the past. As a result we have a legacy that there is no harm in thinking some deity is behind all that happens – good or bad, or that seeing a black cat is a portent of bad things.

The trouble now is that this predilection to consider all sort of extraneous observations might be a ‘sign’ is that it seriously detracts from the real signs which are all around us for the observing. Consider climate change, population growth or loss of biodiversity. Unlike the berry example the benefit of the lesson is not quickly reinforced by those that hold it. The lesson is not absorbed and integrated in one or even two generations so it does not persist in the same way. This slow evolution of knowledge about these complex issues might just result in our extinction if the change happens faster than the time required to get the understanding and the remediation.

I am an optimist but the lack of vision from Copenhagen does not bode well for the future of life on Earth.