Happy New Year!

bernie
Originally uploaded by island_girl.

Hello everyone!

Welcome to the Year of the Dog!

Gong Hei Fatt Choy!!!

Keep smiling!

Baby Watch

These are some pictures I took of him at four and a half months. He's a big baby! And very smiley too. I haven't heard him bawling his eyes out even once. The other day, he was taken out by my mom and even collected a few advance ang pows! Sigh.. being cute will get you everywhere nowadays.

He can't sit up on his own yet, but this little comfy chair props him up without having him falling over. He can't do it for too long though. I usually dump him there and turns the mobile on so he can sit and watch little Pooh characters whiz past him while I get ready to leave the house.

More pictures....

News

When sick is good...

Spy vs spy

Dang it...

phd horoscopes
Originally uploaded by island_girl.

From PhD comics

Foxy company

Talk about cats amongst the pigeons, here's a fox amongst the crows... picture taken along the upper riches of the Thames, near Richmond.

Wouldn't it be nice

Wouldn't it be nice if we were older
Then we wouldn't have to wait so long
And wouldn't it be nice to live together
In the kind of world where we belong

You know its gonna make it that much better
When we can say goodnight and stay together

Wouldn't it be nice if we could wake up
In the morning when the day is new
And after having spent the day together
Hold each other close the whole night through

Happy times together we've been spending
I wish that every kiss was neverending
Wouldn't it be nice

Maybe if we think and wish and hope and pray it might come true
Baby then there wouldn't be a single thing we couldn't do
We could be married
And then we'd be happy

Wouldn't it be nice

You know it seems the more we talk about it
It only makes it worse to live without it
But lets talk about it
Wouldn't it be nice

~~~~~~~~

Thought I'd post up the lyrics to this great song , after surfing through BBC news and coming across this article. Ahh... the sweet optimism of youth, before life gets in the way.

Signed up for a Japanese class that promises to be a 'Hilarious Language Study with Interesting Japanese Cultural Talks' with Mingko today.

What does it all mean? Look out for a series of 'knock knock' jokes in Japanese, coming up next month ;)

No more Casuarina

Am in the lab after an afternoon of mahjong playing at applecow's.

I think MJ fever is spreading like wild fire amongst my friends, and even fatfreddy has gotten into the act too! And not just mahjong either, thanks to my friend HL. It's a good thing he's off skiing next week and not in Singapore for the annual Chinese New Year gambling spree, when every other chinese household in Singapore turns into a mini casino intergrated resort.

Next time, we will need two tables to accomodate everyone nicely. It will be a humourous scene, a mahjong table occupied by one Pinoy (I give up trying to spell Philipino correctly! :P OK.. its F-I-L-I-P-I-N-O), one Ang Moh, an Indian Pakistani and the token manjen, with some of them looking furtively into slips of paper translating the chinese words for the directional tiles and numbers one to ten before deciding which tiles to keep and which to throw out!

After a round which took five hours(!), we adjourned to dinner at the newly renovated Casaurina Prata along Upper Thomson road. And let me put it down on record here:~

This place is over-rated.

S's mee goreng with muttion was not very nice and she could not even plough her way through half of it. My chicken murtabak was OK. I think Zam Zam and Victory make nicer ones. Sometime after placing our orders, we decided that we would also like some fish head curry and I kept emphasizing to the server who took my order that I wanted a small serving, seeing as it was that none of us actually wanted the fish head, but were merely in it for the gravy. He looked as if he understood and went off. In due time, our food arrived, as well as the fish head curry. As he placed it in front of me, the server told me 'this is the smallest we've got'.

Fine. The fish was off just a little bit, but we didn't quite persue the matter, even when the chap came back while we were midway in the meal and asked us if everything was ok. We should have said something about the fish then. Anyway, time for us to get the check and go and I found out that we were being charged $20 for the fish head when it says on the menu that the small serving of fish head was $14. As it turned out, the small serving consisted of half a fish head, and they had run out of small servings and took it upon themselves to give us the large portion without informing us. Feeling rather disgruntled, I went up to the cashier to tell her that we weren't informed of the change in portions and would only be prepared to pay $14 as it was stated on the menu for a small serving. She rang up the server and was told that he had informed us of the no-more-half-fish-head crisis in the kitchen and we had oked the change to the large serving.

What kind of BS was that?? I had five other people who could tell you otherwise! The fish wasn't even fresh! Finally she said, ok.. just pay $16 for the fish head but I said no.. we will pay $14. It really wasn't about the money then, how can any F&B place anyhow suka suka charge us whatever they feel like without even consulting the customer first? In the end she relented because while standing at the cashier counter, I bumped into an acquaintance of mine who incidentally also had some problems with her bill and we talked about what we were standing there for, as you do. It's bad PR for the place.

Suffice to say, Causarina has lost some points with me after this incident. It's no big loss for me, although applecow and BL might have to re arrange their faces or do something equally drastic in order to patronize the place again without the waiters snarling at them or something.

While I'm on the subject of food, here's a place worth plugging; Jeju, a small, nondescript korean restaurant along Seah Street, right next to the Soup Restaurant. Fat Freddy loves the ginseng chicken soup here and everything is reasonably priced, with no taxes included. The chicken soup, for example, costs only $15 and is a portion large enough for two. I also quite dig their vegetable rice dish. The proprieter is this friendly and smiley korean guy and it's a real pleasure dining there. Do check it out!

Greek Mythology and Gene Naming

I subscribe to an Evolution mailing list, in which keeps me updated on post-doc openings, tips and tricks on the lab, as well as other miscellaneous information. Sometimes, someone asks an interesting question and others on the list contribute what they know. Lurkers like me read whatever that catches our interest. Like the following message. It's a rivetting read, (at least for a nerd like me) so I thought I'd share it on my blog.

I've kept the message in its original form, so that the proper people can be credited. Some editing done though, to make it flow better.

******
Email by by Laurence D. Hurst (Professor of Evolutionary Genetics, University of Bath.)

"Many thanks to all who responded, and/or expressed an interest in, the naming of genes after characters from Greek mythology. I cannot claim that the list is exhaustive but as I am now finding it very difficult, through trawling, to come up with new examples, I guess there are probably not so many more. I should like to start by thanking all those who responded (in no particular order): Sarah Cohen, Dmitri Petrov, Jeffrey Marcus, Diana Wolf, Jennifer Gleason, Andy Gardner, Tom Gilbert, Joe Williams, Karl Schmid, Louise Johnson, Diane Ramos, Kristie Mather, David de Lorenzo, Irene Till, Sergios-Orestis Kolokotronis, Roman Arguello, Etienne Patin, Nicole Riddle, Colin Meiklejohn, Jacek Szymura, Chung-I Wu, Hope Hollocher, Jean-Marc Reichart and (my brother) Greg.

Let me commence the run down with the gene that stimulated the original question, Medea, named after the woman who slayed her own children. A 'gene' called Medea exists in the beetle Tribolium (3). In this instance this is a selfish element that causes death of embryos not containing Medea via a maternal effect. So if a mother is heterozygous (+/-) and mates with a -/- father, the +/- progeny survive but the -/- ones die. The offspring killing activity is necessary for the spread of the + allele. In the case of the condition in Tribolium I called it a ?gene? as many selfish elements of this type are two loci in very tight linkage hence behaving effectively as one segregating type (allele). The Tribolium case I suspect was named in part by mythological reference but it is also a convenient acronym: Maternal-Effect Dominant Embryonic Arrest. There is also a Medea gene in Arabidopsis around which a mini-industry of naming after Greek myth has developed. It was rather embarrassing that I forgot about this as one of the workers in this field is all but 50 metres down my corridor
(Rod Scott here in Bath).

Arabidopsis
In the case of the gene in weed, a mutant version of the Medea genes acts possibly via imprinting or as a maternal effect to cause embryo mortality (1, 2). As a mutant copy from the father has no effect, the effect is specifically maternal killing of offspring, hence the Medea reference. Moving upstream, the gene Demeter in Arabidopsis is a regulator of Medea (4). Demeter in Greek myth brings forth the fruits of the earth, in particular she was the goddess of fertility and the growth of vegetation, protector of the earth and its resources, mother of cereals (where she gains her name from the Greek word "dimitriaka") and primarily of grains. As the gene is necessary for seed develoment it seems very appropriate. Medea and Demeter are connected in myth as Medea's arrival in Corinth had saved citizens from starvation, by sacrificing to Demeter and repeatedly appeasing the goddess. The gene Medea in turn regulates Pheres1(5, 6), Pheres being one of the two children killed by Medea.

Like Medea in Tribolium, Artemis (7) in weed seems to derive its name also, at least in part, as an acronym: Arabidopsis Thaliana Envelope Membrane Integrase. If the myth was in the minds of the authors I couldn?t find any reference to the logic. From weed I have found one further putative connection, the gene Argonaute. The gene was named by reference to the squid-like appearance of the leaves of Arabidopsis mutants lacking AGO1 gene function(8). In this case the Greek connection seems to be one step removed. The scientific name of the paper nautilus, especially the largest species, Argonauta argo, is of mythical Greek origin. The argonauts were a group of Greek heroes that, led by Jason, travelled to Kolchis to gain the golden fleece. They were called that way, because their ship was the Argo. In Greek argonaut means "who travels on the Argo". The squid's discoverers probably mistook it's sail-like flaps as a locomotive organ and thus drew the similarity to the mythical Argo. So the Argonaute gene looks to have no direct connection to myth, just to squid-like appearance.

Flies
Despite this flurry in Arabidopsis, it seems, however, that the Drosophilists are most well acquainted with Greek myth. So far I have found 15 namings from Greek mythology. First there is the speciation gene Odysseus (9). Odysseus ordered the making of the Trojan Horse and rode inside along with other warriors.

Chung-I Wu kindly explained that: "The reason [for the naming] was somewhat silly. We were looking for something that could wreak havoc in a foreign territory. Odysseus hiding in a wooden horse is like the gene embedded in the introgression; the result was devastating."

Carrying on with the Odysseus connection, many of the Greek inspired names in flies are transposable elements. Some have expressed the opinion that this all started with D. virilis transposable elements being named after characters from the Odysseus (Ulysses, Penelope, Helena, Paris). The first one was Ulysses (11, 12) (a traveller's name is appropriate for a transposable element) and then the co-mobilized TEs were given names that were somehow related to Ulysses. Naming transposeable elements in flies after Greek mythological characters is now very common: see Circe and Hercules, Minos and Hermes (the later first reported in Musca domestica).

Moving off transposable elements, the Persephone (10) gene encodes a serine protease in Drosophila. It was given this name (Pr. Jean-Marc Reichhart pers comm.) because the mutation was found in a lethal suppressor screen. Just as the Greek godess was able to cross the Styx and take dead people to live again, the mutation allows dead necrotic flies to live.

Hades, alias Gram-negative bacteria binding protein 3, is involved in immune activity. The usage of the name Hades seems relatively rare (most appear to refer to GNBP3) but some do use the name (see e.g. (13)). I have as yet been unable to track down first usage or the reason for the name. Sorry.

Scylla and charybde (14) (a. k. a. charybde) are paralogous genes identified as growth suppressors. The genes are named after mythological monsters said to have lived in the Strait of Messina between Sicily and Italy that endangered shipping. Quite why genes whose simultaneous loss results in flies that are more susceptible to reduced oxygen concentrations and that show mild overgrowth phenotypes, should be named after monsters I have yet to uncover.

Much clearer is the naming of Ariadne this being a Drosophila gene (15) necessary for nerve cell axons to reach their targets. Its human and mouse orthologs have been characterized. Ariadne, in Greek mythology, helped the Athenian prince, Theseus (Thisseas), son of Aegeas, to escape from the Cretan Labyrinth. She gave Theseus a ball of string which he attached to the entrance of the Labyrinth, so that he could find his way back out. The idea of something that helps something else find the way seems to be the connection here.

Last, but by no means least, Sphinx (16) in D. melanogaster is a new gene and a chimera of two others. The name was chosen (16) to invoke an analogy to another chimera, the Sphinx from ancient Greek legend having a lion's body and a human head.

Mammals

By contrast to the fly world mammalian gene only rarely get named after Greek myths (or at least the trawl found only a few). The gene Klotho (17) is associated with premature aging in mice and variation in klotho function contributes to heterogeneity in the onset and severity of human age-related phenotypes. Klotho was one of the three Greek Fates -- goddesses who in Greek mythology controlled a person's destiny and lfe. Klotho, whose name means "spinner", spun the thread of life. Lachesis measured the thread and Atropos cut it.

A further case of a very deliberate reference comes in the case of the Hephaesin gene named after Hephaestus, the Greek god of metal-working. He wove a net of iron, and ensnared the illicit lovers Ares and Aphrodite making love. Correspondingly Hephaesin gene in mice facilitates transport of iron from the intestines into the body's circulatory system (18). When the gene is mutated iron cannot be transported to the blood, and iron-deficiency anemia occurs.

In the original email I noted Callipyne in sheep but thought it unrelated to myth. Thanks to Sergios-Orestis Kolokotronis for putting me straight here: callipyge does refer to Greek mythology, it is one of Aphrodite's surnames "Aphrodite Kallipyge", but I was right in that it does mean beautiful buttocks. The gene derives it name from the phenotype associated with overgrowth of buttocks (see e.g. (19, 20)).

Other taxa

Aside from mammals, flies and weeds the use of Greek myth seems to be relatively sparse. The gene Cerberus (21), can induce ectopic heads in Xenopus and so is named after the three-headed guard dog of Hades. Othologs are known in mice and humans, also referred to as Cerberus (e.g. (22, 23)). Caronte (24, 25) in chickens is a member of the Cerberus family. This seems to be a strange case of the same gene being identified by three independent groups (see also (26)), two of the independently calling it Caronte. According to the authors of one of the reports (24): "We have named this gene Caronte (Car) after the mythological boatman who shuttles souls to the underworld, where the dog Cerberus dwells."

The other group specifies that they use the same logic (25). May be there was some collusion. Similarly in fish a putative ortholog of caronte is known as Charon(27). In fish the gene Cyclops (28) is associated with cyclopedia, a condition which gets its named from the one-eyed monster.

Finally, from the world of molecular biology comes the lambda Charon
phage (e.g. (29)). I have found claims that the naming is derived from the Greek: "For a typical lambda phage vector, the insert usually must be at least 12 kb and not over about 20 kb. This size range makes lambda phage vectors particularly useful for genomic libraries (collections of phage containing all of a genome in 12-20 kb fragments). Lambda phage vectors of this sort are sometimes called Charon vectors, a reference to Greek mythology, in which the boatman Charon ferries the souls of the dead across the River Styx." From: http://www.colorado.edu/MCDB/MCDB2150Fall/notes00/L0015.html. I have been unable to track down first usage to confirm this, but it seems plausible.

Non-Greek myth

There are several genes derived from other non-Greek myths but here my list is much less exhaustive. For example, in Arabidopsis there is a gene named after the Etruscan goddess of fertility Feronia (30). The gene disrupts the female gametophytic control of pollen tube reception.

From roman myth come the two paralagous genes named janusA and janusB in Drosophila, which were named because they are right next to another
gene (Serendipity) but they face in the opposite direction from Serendipity, so this is reminiscent of the two-faced roman god Janus. A third paralagous gene in this group is named ocnus, after the grandson of Janus.

Moving east, jingwei (31) comes from an ancient legend from china
(San Hai Jing). Jingwei, a daughter of Emperor Yande, first Chinese emperor 30000BC (sic), tragically drowned while swimming in the East China Sea. Jingwei was then reincarnated as a beautiful bird that drops stones and wood into the sea in an attempt to fill it, thus preventing others from drowning."

Also from China comes monkey-king (32) after a mythical monkey king in ancient China who could transform his hair into many offspring." From Egypt comes Osiris and Isis (33) again in flies. Osiris was so called because the Isis locus partially rescues the effects of trisomy of the region containing Osiris."


Literature cited
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(1997) Mutation of the mouse klotho gene leads to a syndrome resembling
ageing. Nature, 390, 45-51.
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ceruloplasmin homologue implicated in intestinal iron transport, is
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Steele, M.R., Barendse, W., Green, R.D. and Georges, M. (1994)
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(1996) Cerberus is a head-inducing secreted factor expressed in the
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Antagonistic signaling by Caronte, a novel Cerberus-related gene,
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J., Ortiz, A. and Izpisua Belmonte, J.C. (1999) The novel Cer-like
protein Caronte mediates the establishment of embryonic left-right
asymmetry. Nature, 401, 243-51.
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Stern, C.D. and Levin, M. (1999) Cerberus regulates left-right
asymmetry of the embryonic head and heart. Curr. Biol., 9, 931-938.
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T., Hibi, M. and Suzuki, T. (2004) The Cerberus/Dan-family protein
Charon is a negative regulator of Nodal signaling during left-right
patterning in zebrafish. Development, 131, 1741-1753.
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(1998) Induction of the zebrafish ventral brain and floorplate requires
cyclops/nodal signalling. Nature, 395, 185-189.
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Expression of the Escherichia coli cell division gene sep cloned in a
lambda Charon phage. Science, 206, 220-2.
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Arabidopsis mutant feronia disrupts the female gametophytic control of
pollen tube reception. Development, 130, 2149-59.
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Meme from Recent Runes

Waah.. I kena tagged by Ivan from Recent Runes! Well.. I'm sure its not the first time someone tagged me for a meme (I vaguely remember Mr Budak attempting to tag me once, but somehow I never got around to it after mentally filing it away.. oops!)

Ok.. so here's my first meme! Very quickly now..

What were you doing ten years ago?
A medi-shield clerk at Mount Elizabeth Hospital

What were you doing one year ago?
This day last year? I was freaking out over a conference presentation that looked like this and spent the last half of january in Ilo Ilo, Philippines. A short recap here.

Five snacks you enjoy
1. Kit kats (made in any country except Malaysia)
2. Garuda brand kacang atom (pedas) --- This rawks!
3. Strawberry pocky (made in Japan ones only)
4. Salt and vinegar crisps
5. Home fried keropk udang with sambal (my friend Irene fries really yummy ones)

Five songs to which you know all the lyrics off your head right now
1. Angel eyes by Jeff Healy Band (my favourite soppy song of all time)
2. Jesus loves me (Sunday school staple)
3. Happy Birthday song (duh)
4. Que Sera Sera
5. Puff the magic dragon

Five things you would do if you had one million dollars
1. Buy my own place and do it up
2. Give some away (to charity, my parents)
3. Invest some
4. Travel
5. Work for free (no more grovelling for funding!)

Five bad habits
1. Easily distracted
2. Untidy
3. Tactless
4. Always reading too many books at the same time
5. Looking detached when I shouldn't

Five things you like doing
1. Good food and wine with good company
2. Beach combing
3. Chilling out
4. Playing mahjong!
5. Cloud watching

Five things you would never buy, wear or get new again
1. Spandex - it's a privilege, not a right!
2. Levi's jeans
3. Floral culottes (eeeuugh!)
4. Knee high boots (again, a privilege, not a right)
5. Extremely gu-niang clothes in general (although I am partial to pink stuff)

Five favourite toys
1. My panasonic lumix FX9
2. My lau kok kok 3G 30gb iPod
3. My recently resurrected G4 Tibook
4. My Mogu dog
5. My nephew :P

I don't have many blog friends to tag this on to (they all got tagged too! So it ends here. Boo) I had fun though. :D

MoK

'So how come you never go to that Ministry of Sound? Very long queue you know.. that night all the way until Liang Court!!'

The taxi driver asked when we got on the taxi from Heeren where we had been hanging out at Balcony to head towards Plaza in by the Park.

And FF tells the taxi man how MoS is opening clubs in Asia cos "no one 'cool' goes to MoS London anymore". I wasn't in any position to say anything, as I 1) am not 'cool' and 2) don't know the clubbing scene in Singapore, much less London

As we got to our destination and prepared to leave, he turned around and said 'Ya! Don't go to Minstry of Sound! Ministry of Kopitiam better!'

We agree. Mmmmm....xiao long bao!

Mystery solved!

Befuddled by Mornington Crescent?

Well, fret no more! In the wake of all this Tony Robinson Da-Vinci-code-grail-hunting business, someone has finally rolled up his sleeves and done the same intrepid investigative work with this much loved but often confusing game. Graeme Garden separates the facts from the myths! Travels back in time to see how the Victorians play it! Ancient rules and history, this programme will reveal all.

I don't know how to link the show but here's the link to the page. Click play. Good for this week!

Eating from one year to the next

Happy New Year everyone! So what did you do on the last evening of 2005?

I literally ate from the 'old year to the new' 8.30pm 31st December till 12.30 1st January. Very auspicious start, by Chinese standards, thanks to Mr and Mrs T, who very generously hosted me and five other guests for dinner at their home. No pictures, for the broken camera is still in the shop (boo), but trust me, it was a veritable feast! Let's just say that at this very moment, 22 hours after I've stopped eating, I am still full from all that food. I kid you not.

And yes, I must say the roast duck is absolutely delicious! And I also liked the side of cucumber salad. (Note to self: Must ask Mrs T what the dressing is...) All this was accompanied by a really yummy seafood fried rice and angel hair pasta (thanks casey!!!) and washed down with wine, courtesy of Mr T, KK and Casey. Every new bottle of wine opened sparked off an animated conversation between them (Old world? New world? Shiraz? Pinot noir? Burgundy?). As for me, I just drank feeling quite sheepish that all this good wine was wasted on me, but I did glean some insights about wine appreciation from KK, so I guess there is hope for me yet. :P

That's quite alot of food, you must be thinking at this point.

Yes, that's what we thought too! And we were more than happy stuffing our faces with the lot, but wait, there's more!!! A sumptious sukiyaki hotpot with home made stock. Loads and loads of tender beef slices, pork belly, cooked with sliced leeks, lotus roots, bamboo shoots amonst other delectable veggies and tang hoon that soaked up the sweetness of the sukiyaki sauce. It's got me thinking that I should try this too, instead of the usual steamboat dish this lunar new year. The way Mrs T put it, it sounds really easy. I've planted the idea of a sukiyaki reunion dinner in sis's head. Hopefully she'll take the bait. hehehehe.

And before you think that's it, there's still dessert to go! Ever the perfect hosts, Mr and Mrs T offered 2 types of dessert, first up, barley soup with beancurd skin, quail eggs, wintermelon sugar and ginkgo nut, accompanied by a lovely dessert wine, and after ushering in the New Year proper with our bubbly, Mr T presented us with another temptation - cranberry and orange cake from Cedele's! And we inhaled it too....

Hey... its the New Year after all. :P

I was ready to collapse from all that food and Mr T came to the rescue again, this time with a much needed brew of Pu er to really wash all that food down, accompanied with conversation and fussing over the dogs.

Thank you Mr and Mrs T, for inviting me around for dinner! And I forgot to bring these two jars of condiments I brought England. :S Never mind, will give it to you next week. See you then!