Thursday, 26 February 2009

Seafood dilemma

I'm having a dilemma over seafood at the moment. I really love good, fresh seafood, although I don't tend to eat a lot of it. But it seems lately that the more I read, the less I feel I ought to eat. This despite the fact I'm constantly hearing on the news that seafood and fish oils are so good for my health and that most people don't eat enough of them.

In a typical week, the only seafood I am likely to eat is some canned tuna or a fresh piece of salmon, maybe a different fresh fish if something else looks good at the markets. If I lived at the coast that might be different though. I'm very careful to avoid species that I know are being unsustainably harvested, such as orange roughy. I know that salmon and tuna aren't perfectly managed either, but I've generally considered them to be better fish to eat from a conservation perspective. But this week I've read several things that have made me think I may be wrong. Perhaps I should give up on fish altogether? Here are some things to think about:

1) On Southern Fried Science, a really interesting post about why "Dolphin friendly" tuna might not be very friendly to anything else apart from dolphins - so maybe I should cut back on the tuna after all?

2) But maybe there is some hope? Tuna fisheries are also notoriously unkind to albatross populations, especially long-line fisheries. The birds try to eat the bait, get caught in the hooks and drown. I have always felt some guilt for these unseen deaths when eating my tuna mayonnaise. Then today I read on The Great Beyond that albatrosses may be saved after all. Changing practices have lead to an 85% decrease in the number of albatrosses killed by the fisheries. This can only be good news, surely?

3) I've also found another reason to worry about eating salmon. BBC Wildlife Magazine has an article in the February 2009 issue (page 39) describing a decline in salmon numbers in British Columbia. Fewer salmon means less food for grizzly bears for starters. So why are the salmon declining? The article points the finger at overfishing and the effects of fish farms on wild fish: sea lice breed in the farms then move out to infect wild fish. The salmon I get all comes from Aussie waters, mostly Tasmanian, but even though there are no bears to go hungry I'm sure the farms have the same problems. Perhaps I shall rethink salmon too?

I think I might just have to fork out a few dollars and get myself a copy of the Australian Marine Conservation Society's Sustainable Seafood Guide. At least then I'll have a better idea where I stand.

Finally, to end this post on marine life, I loved reading about this  in the Telegraph: a biologist on a tagging trip caught a huge stingray, 7 foot by 7 foot!!!

Monday, 23 February 2009

BBC book meme

I've done a few of these meme quizzes over on Facebook lately and I wasn't going to do any more of these things for a while, but this one was quick to do and vaguely intellectual. I stole it from Sciencewomen. I haven't claimed any books that I read at school that I can't remember enough to know the storyline. Not bad, I've read 32 of them. I must have non-average tastes though as a lot of my favourite books are missing from the list, although some childhood favourites are there. Looks like I need to brush up on my BBC period dramas...


1) Look at the list and put an ‘x’ after those you have read.

2) Add a ‘+’ to the ones you LOVE.

3) Star (*) those you plan on reading.
NB I've added an F if I've seen a film or a stage version but not read the book.

4) Tally your total.

1. [ ] Pride and Prejudice Jane Austen
2. [x,+] The Lord of the Rings JRR Tolkien
3. [ ] Jane Eyre Charlotte Bronte
4. [x] Harry Potter series JK Rowling
5. [F ] To Kill a Mockingbird Harper Lee
6. [x] The Bible (some may be surprised at this!)
7. [ ] Wuthering Heights Emily Bronte
8. [ ] Nineteen Eighty Four George Orwell
9. [F] His Dark Materials Philip Pullman
10. [ ] Great Expectations Charles Dickens
11. [x] Little Women Louisa M Alcott
12. [*] Tess of the D’Urbervilles Thomas Hardy
13. [ ] Catch 22 Joseph Heller
14. [x, well, lots of them anyway, not sure if all] Complete Works of Shakespeare
15. [ ] Rebecca Daphne Du Maurier
16. [x,+] The Hobbit JRR Tolkien
17. [ ] Birdsong Sebastian Faulks
18. [ ] Catcher in the Rye JD Salinger
19. [ ] The Time Traveller’s Wife Audrey Niffenegger
20. [ ] Middlemarch George Eliot
21. [ ] Gone With The Wind Margaret Mitchell
22. [ ] The Great Gatsby F Scott Fitzgerald
23. [ ] Bleak House Charles Dickens
24. [ ] War and Peace Leo Tolstoy
25. [x,+] The Hitch Hiker’s Guide to the Galaxy Douglas Adams
26. [ ] Brideshead Revisited Evelyn Waugh
27. [ ] Crime and Punishment Fyodor Dostoyevsky
28. [ ] Grapes of Wrath John Steinbeck
29. [x] Alice in Wonderland Lewis Carroll
30. [x] The Wind in the Willows Kenneth Grahame
31. [x] Anna Karenina Leo Tolstoy
32. [x] David Copperfield Charles Dickens
33. [x] Chronicles of Narnia CS Lewis
34. [ ] Emma Jane Austen
35. [ ] Persuasion Jane Austen
36. [x] The Lion, The Witch and The Wardrobe CS Lewis
37. [*] The Kite Runner Khaled Hosseini
38. [F] Captain Corelli’s Mandolin Louis De Bernieres
39. [F] Memoirs of a Geisha Arthur Golden
40. [x] Winnie the Pooh AA Milne
41. [x] Animal Farm George Orwell
42. [F] The Da Vinci Code Dan Brown
43. [x,+] One Hundred Years of Solitude Gabriel Garcia Marquez
44. [ ] A Prayer for Owen Meaney John Irving
45. [ ] The Woman in White Wilkie Collins
46. [x] Anne of Green Gables LM Montgomery
47. [ ] Far From The Madding Crowd Thomas Hardy
48. [*] The Handmaid’s Tale Margaret Atwood
49. [x] Lord of the Flies William Golding
50. [ ] Atonement Ian McEwan
51. [*] Life of Pi Yann Martel
52. [ ] Dune Frank Herbert
53. [ ] Cold Comfort Farm Stella Gibbons
54. [ ] Sense and Sensibility Jane Austen
55. [ ] A Suitable Boy Vikram Seth
56. [ ] The Shadow of the Wind Carlos Ruiz Zafon
57. [x] A Tale Of Two Cities Charles Dickens
58. [ ] Brave New World Aldous Huxley
59. [*] The Curious Incident of the Dog in the Night-time Mark Haddon
60. [*] Love In The Time Of Cholera Gabriel Garcia Marquez
61. [ ] Of Mice and Men John Steinbeck
62. [ ] Lolita Vladimir Nabokov
63. [ ] The Secret History Donna Tartt
64. [x,+] The Lovely Bones Alice Sebold
65. [F,*,+] Count of Monte Cristo Alexandre Dumas
66. [ ] On The Road Jack Kerouac
67. [ ] Jude the Obscure Thomas Hardy
68. [F] Bridget Jones’s Diary Helen Fielding
69. [ ] Midnight’s Children Salman Rushdie
70. [ ] Moby Dick Herman Melville
71. [x] Oliver Twist Charles Dickens
72. [ ] Dracula Bram Stoker
73. [x] The Secret Garden Frances Hodgson Burnett
74. [x] Notes From A Small Island Bill Bryson
75. [ ] Ulysses James Joyce
76. [ ] The Bell Jar Sylvia Plath
77. [x] Swallows and Amazons Arthur Ransome
78. [ ] Germinal Emile Zola
79. [ ] Vanity Fair William Makepeace Thackeray
80. [ ] Possession AS Byatt
81. [x] A Christmas Carol Charles Dickens
82. [ ] Cloud Atlas David Mitchell
83. [ ] The Color Purple Alice Walker
84. [F] The Remains of the Day Kazuo Ishiguro
85. [ ] Madame Bovary Gustave Flaubert
86. [ ] A Fine Balance Rohinton Mistry
87. [x] Charlotte’s Web EB White
88. [ ] The Five People You Meet In Heaven Mitch Alborn
89. [x] Adventures of Sherlock Holmes Sir Arthur Conan Doyle
90. [x,+] The Faraway Tree Collection Enid Blyton
91. [ ] Heart of Darkness Joseph Conrad
92. [ ] The Little Prince Antoine De Saint-Exupery
93. [ ] The Wasp Factory Iain Banks
94. [x] Watership Down Richard Adams
95. [ ] A Confederacy of Dunces John Kennedy Toole
96. [ ] A Town Like Alice Nevil Shute
97. [F,*] The Three Musketeers Alexandre Dumas
98. [x] Hamlet William Shakespeare
99. [x] Charlie and the Chocolate Factory
100. [F] Les Miserables Victor Hugo

Thursday, 19 February 2009

Eaten to extinction?

Another entry for the eaten to extinction section, this time via an article on National Geographic news.

Worcester's buttonquail, known to science only through decades-old museum specimens, was thought to be extinct. Then in January a TV crew, filming at a market in the Philippines, captured one of the birds on camera. The bird was subsequently sold for food. I hope whoever bought it enjoyed their meal. Of course if there is one bird at the market, there is a chance there are others still alive in the wild, although perhaps not many. So the species may not be extinct after all... but realistically, what is its chance of lasting much longer...?

Wednesday, 18 February 2009

In the news today

Some sciencey stories that have caught my eye this week:

A paper in Genome Research describes the sequencing of the entire mitochodrial genome of the extinct thylacine or Tasmanian tiger. This probably deserves it's own post: it uses new methods and the results are surprisingly different from the sequences previously available. I'll try to review it in more depth later...

Scientific American reports on the discovery of two species of fly in Namibia which are members of a genus previously only known from the fossil record. This is pretty cool, especially given my personal soft spot for Namibia. Maybe I have unknowingly inhaled one of these flies! I am however a little disappointed that the good folk at Scientific American have described the flies as "living fossils". The term is not helpful. If a fly is alive it isn't a fossil. And where should the line be drawn? Many extant species have close relatives known from the fossil record. Are they all "living fossils"? How much divergence is required before they are no longer classed as "living fossils"? I think terms like this can really confuse people.

ABC news reports on the births of ten Tasmanian Devil pups on an island sanctuary. The pups are the offspring of devils chosen for captive breeding because of their good genetics. They have similar genetic profiles to the famous Cedric, a devil who raised, then dashed, the hopes of researchers by first showing immunity to the devastating Devil Facial Tumour Disease, only to later contract the cancer. Maybe these pups will show greater resilience to the disease?

And finally I can't resist posting a link to this: BBC footage of bears catching dead fish with their feet! Apparently they don't like to get their ears wet :-)

Thursday, 12 February 2009

Darwin Day

As I described in my previous post, I've not been in quite the right frame of mind for blogging these last few days, my thoughts have been elsewhere. So my planned post for Darwin Day has been deferred as I've not put in the necessary reading. But I still wanted to mark the occasion. Today is the 200th anniversary of the birth of Charles Darwin. Darwin Day is "a global celebration of science and reason" held around Darwin's birthday each year. This year is also the 150th anniversary of the publication of "On the Origin of Species...". At work we celebrated with Darwin-themed cakes and a few candles. But I said I'd blog today... can I come up with something interesting on the fly?

After all these years, how does society regard the legacy of Darwin? That's what I wanted to cover. I could list the essential contribution of Darwin's ideas to the development of modern biology and analyse Theodosius Dobzhansky's assertion that nothing in biology makes sense except in the light of evolution. I could debate the future for evolutionary thinking and science in the US under the new Obama government, challenged as it is by the creationist and intelligent design lobbies. But so many others have written good, thoughtful posts on these topics already and here, in the last couple of hours of Darwin Day in Australia, I don't have the time to come up with any deep thinking or novel insights of my own. So I'll turn, as do so many of my generation (and so many of my students) to Google for some insight. I've just this moment performed a Google search for "Charles Darwin". If anything will reflect the popular legacy of Darwin today it will surely be the top ten hits I get on Google... right?

First up is a news story from the Telegraph in England. Darwin's home, Down House, is re-opening to the public on Darwin Day, following renovations. So Darwin is sufficiently well known and interesting that people will travel and spend money to see where he lived. I guess that is nothing surprising, but perhaps encouraging for Darwin fans to know that people care.

Second is Wikipedia, of course. But Google anything today and you will surely get a Wikipedia entry in the first few hits, so not much to glean from this.

Next is This is one of many websites dedicated to the man. Here you can find info on his life, his travels, his writings and people he knew and worked with. Today the homepage is decorated with a birthday cake and balloons. I wonder if he would have appreciated the thought?

Fourth is a biography of Darwin at Lucidcafe. It is short but seems to cover the basics well as far as I can tell at a glance and there are plenty of related links.

Fifth is a link to a list of blog posts on Darwin. This doesn't surprise me, especially today, as he pops up everywhere in the blogosphere, in scientific blogs and in blogs on what I shall simplistically refer to as "evolution vs religious fundamentalism". Likewise, the sixth is a link to a list of Darwin's books. Again, no great surprise.

Finally, the seventh hit, we get to that wonderful resource: The complete work of Charles Darwin online. Want to know what Darwin wrote about something? Look here. It's open access and it does what it says on the tin, with a handy user guide.

In eighth and ninth are two more brief biographies and in tenth a link to "On the Origin of Species..." on Google Books.

So, most of the top ten hits are either biographical links or academic links to Darwin's writings. I like this. Darwin was an academic and it seems only correct that the top ten hits (realistically this is as far as many people will look) include so many links to the works of the man himself. Amongst all the serious scholarship, so much rubbish is written today about what "Darwinism" really is that it can be hard for those new to evolutionary theory to figure out which sources to trust. So where better to start than with what he actually said. Then take it from there.

Out of interest I scrolled through a few more pages of results and found mostly more of the same. A mention perhaps to the Charles Darwin Foundation for science in the Galapagos at number 12, and Charles Darwin University in Australia at number 15. Nice to see his name is out there still.

Bushfires in Victoria

I haven't posted for a few days. I meant to, on several things, but like the rest of Australia I have been in thrall to the news of the Victorian bushfires. I am nowhere near Victoria, but it's truly a national disaster. For many Australians this could so easily be on our own doorsteps. At present over 180 people are confirmed dead and well over 1,000 homes lost. This is the worst natural disaster in the history of the Australian nation. I am not sure what more I can write and other topics have seemed a little trivial until now.

In January 2003, bushfires destroyed over 500 homes and killed four people in Canberra, the Australian capital city. We were living in Canberra then, in a suburb not directly affected, but close enough to the action to be on evacuation standby. We were in town on that fateful day and watched the firefighting helicopters flying back and forth, from lake to fire front, over and over. We escaped unscathed, but friends lost their houses and everything in them.

To give an idea of the scale of the Canberra fires, and how bad it must have been for the people in the heart of both these and the current Victorian fires, here are a couple of photos I took in 2003. The first is taken near the city centre about 1pm on a summer afternoon. We went to a movie and walked outside to drive home through this.

The second photo is taken from our suburb. The fire was stopped from crossing a major road just the other side of the hill in the picture - otherwise we'd have had a different story.

Nothing else to write on this right now. My thoughts are with those who have lost loved ones and their homes in Victoria this week.

Thursday, 5 February 2009

As we're on the topic of snakes...

...the news today is full of stories about a very big snake. In Nature this week there is a paper describing the largest snake ever discovered: a a 60-million-year-old South American Titanoboa. Sounds like a snake I might not be so keen to meet up with. Being the slacker I am I haven't got to the actual paper yet, but news stories are here, here and here.

Tuesday, 3 February 2009

A snake and a quoll

I've just been away for a few days, visiting people in Tasmania. It was a nice trip and I hardly went near the internet. Hence no blog posts. It was also a bit of a reminder of the somewhat cloistered world I must live in, sheltered amongst scientists and other like-minded people as I am in my usual daily life. I am clearly a bit of a science geek. My reason for making this statement about this trip? It was great to see people I haven't seen for a while and spend time doing fun things, but the absolute highlights of this trip for me were two fleeting wildlife encounters. 

The first was a tiger snake encounter in a garden. Most other folk there at the time were not happy to see the snake and there was some talk of the only good snake being a dead snake. Perhaps the snake heard because it promptly moved on. Now don't get me wrong, I'm not a crazy herpetologist and I am mostly definitely VERY scared of venomous snakes. I acknowledge that the snake was rather close to peoples' houses and it's probably better for them that it wasn't so close and they'd be a lot happier if it was moved elsewhere. I was certainly very careful where I put my feet for the next few days. But still, above all else it was just a wonderful thing to see. Here, judge for yourselves:

The second wildlife encounter was, if you can believe it, even more fantastic than the snake. Actually I'm sure a lot of people would find this the more favourable option. This because it involves a cute furry mammal. I saw a quoll! I have never before seen a quoll in the wild, although I've been in the right sorts of places many times. So this was very exciting. We were driving to the airport early in the morning. It was still dark and we were paying close attention to the roadside vegetation for fear of colliding with suicidal wallabies, when what should saunter across the road in front of us but an unmistakably spotty quoll. It was an Eastern quoll, I know this because it was black with white spots. We had to pretty much stop the car to avoid hitting it. It was only a quick look, but it made being up and about at 4am most definitely worthwhile!

Wednesday, 28 January 2009

In the news today

Well, there are lots of things in the news today of course, but two in particular caught my eye.

First, one of my all-time favourite people I've never met, Sir David Attenborough, on receiving hate mail from religious fundamental types. Sir David Attenborough: 'I get hate mail telling me to burn in hell for not crediting God'.
Sir David also said it was "terrible, terrible" when creationism and evolution were taught in schools as equivalent, alternative perspectives.

"It's like saying that two and two equals four, but if you wish to believe it, it could also be five... Evolution is not a theory; it is a fact, every bit as much as the historical fact that William the Conqueror landed in 1066."
I'm with Sir David on this one!

Second, a bit of "well I never!" or "how cool is that!". A NSW couple got to see a red belly black snake eat a brown snake - cool enough alone you might think - but THEN the brown snake managed to escape from the belly of the red belly black by exiting head-first from its mouth. Now that is seriously cool!

Mr Barton reckons that somehow the brown snake turned itself around inside the black snake.

"When you tell these stories no-one believes you, but I have the photographs," he said.

I have seen both these snakes in the wild, but never doing anything quite so exciting. Although S did a good job of almost stepping on a brown snake on a bushwalk late last year - that was exciting for us! Here's a nice red belly black I befriended (from a safe distance) at Jervis Bay a couple of years back:

Tuesday, 27 January 2009


Specifically, motivation to go in the lab and do science. It is lacking today. Possible causative factors:

1) I am suffering post-public-holiday-itis, an extreme form of Monday-itis brought on by the long weekend. A possibility, but unlikely to be the full story? I'm not lacking motivation for other work-related tasks.

2) I am lacking motivation to move in general because my neck and shoulders are achy and I have arranged to see my physio. So the idea of repetitive pipetting is unattractive. I think there is some truth in this one.

3) I am still crabby, despite my years of professional experience and knowing not to take it too personally, that the PCR I ran on Friday has to be repeated. There is a faint but definite band in one of my negative controls. This is not the end of the world: I know that the nature of the samples I work with and the type of reactions I do make me a prime candidate for occasional contamination and I have ways to deal with this, but it still makes me grumpy. Especially when it happens on a Friday afternoon. At heart I think this is the real cause of my apathy today.

I have an hour before I have a meeting. I should go to the lab. Now. Really.

Monday, 26 January 2009

Australia Day

Today is Australia Day and so a public holiday long weekend during which I have done NO SCIENCE. I have at least spent a fair chunk of time catching up with some sciencey blogs I have neglected. I am still getting used to public holidays unaccompanied by thesis-guilt, although I am sure that unfinished-manuscript-guilt is lurking somewhere in the background waiting to surprise me as I turn a corner or open a closet.

Australia Day is always an interesting exercise in cultural observation to me as a person who grew up elsewhere. For many folk I know, the national day is devoted to stereotypically Aussie activities such as barbecues, cricket, spending time with mates, going to the beach and drinking beer. It's usually a pleasant day for me, although I'm not decided where I stand in the debate on the appropriateness of January 26th as Australia Day. Today is the anniversary of the arrival in Australia of the First Fleet of colonising Europeans and as such is considered by some as more of an Invasion Day. I have to say I can see their point...

So how did we choose to mark the occasion? Well, nothing too extravagant: a lazy breakfast, as befits a public holiday Monday, then out for lunch at the fab Ironbark Cafe which is not too far out of our way for a visit. They specialise in Australian food, including native Australian ingredients and had live music and specials for the national day. But we were a bit boring as on this occasion we both wanted a favourite: beer-battered flathead (fish) fillets with a native Aussie salad and chips. The chips come tossed in tasty Aussie bush spices...mmmm. I also have a very soft spot for the native lime soft drink, conveniently just out of frame in my photo below.

If you're ever in the area, try it, I doubt you'll have had comparable food elsewhere (but if you have please tell me where). So, it was a nice quiet day out then home for a cup of tea, a book and watching the Aussies lose to South Africa at cricket. Perhaps not the Australia Day they were hoping for...

Endangered delicacies

It wasn't perhaps the main intention when setting up this blog, but I am starting to think I will post regular updates on species in danger of extinction as a consequence of human gastronomic tastes. This decision is prompted by an article I encountered today on Biology News Net titled Frogs are being eaten to extinction, which reports on recent research from the University of Adelaide.

Sunday, 25 January 2009


Given my interest in wildlife conservation, I thought it only right to make my first sciencey post a comment on extinction, or what happens when wildlife conservation fails. One of the best-known extinct species in the popular mind is, of course, the dodo. I won't rehash the story of the dodo here, it has been covered in detail elsewhere. But as a quick summary: the first accounts of dodos came from Portuguese visitors to the then-uninhabited island of Mauritius in 1507. The Dutch colonised the island in 1638. By the end of that century the dodos were gone.

The 2008 IUCN Red List will tell you that the dodo is one of 717 known animal species to have become extinct since their records begin. Some of these extinctions are shamefully recent events, for example the extinction of the baiji dolphin only a few years ago.

Reading about human-mediated extinctions reminds me why I do the work I do. Perhaps it is a futile hope in the society we live in, but I hope that something I do might one day make a difference to some species on the edge. I study Australian wildlife, haunted by the ghosts of the thylacine and the 26 other Australian mammals driven to extinction since 1788 (not to mention the birds, frogs, insects, plants...). As I travel the country I can only feel the gaps left by creatures such as the toolache wallaby, the desert rat-kangaroo or the remarkable gastric-brooding frog. I've seen Tasmanian devils in the wild and I confess the first time it brought a tear to my eye. On my next trip to Tassie I fear I won't see them as easily and if I do it will be bittersweet: since I arrived in Aus nearly ten years ago they have been ravaged by devil facial tumour disease.

Teaching these topics to first year undergrads saddens me. I think some wonder why we even bother. In the face of the weight of history is it futile to hope that there is a place for conservation in this world? I hope so.

The First Post

I'm new to this. I've been a blog reader before, but not a blog writer. I'm not sure why today was the day to become the proud author of a shiny new blog, but let's see where we end up...

Perhaps an introduction is the place to start. I grew up in England but now I live in Australia with a lovely bloke I will refer to here as S. We have no kids or pets, unless you count the lizards in the garden or the spider that lives in the corner of the kitchen window. I am an academic type. Almost a year ago I submitted my PhD thesis (research themes genetics, wildlife, ecology) and after examination, revisions and administration I finally graduated at the end of 2008, so you can now call me Doctor. Whilst finalising my thesis I vowed that once it was all done I would strive to live a more rounded life and do something more creative: perhaps this blog is the result?

Now I'm working as a postdoc, fully in research at the moment, although I've done some teaching in the past. I might write about some of what I do at work, I'm not sure, but expect to get snippets of my adventures, science and other stuff that I find interesting and an idea of the more mundane side of my daily life in this beautiful hot dry corner of the world.