Friday, September 29, 2006

Another Song

This song was actually written when I was back in Halifax... Acutally a few weeks before I left for BC, which eventually led me here to Australia. Well, I was living in the living room, out of a suitcase, with a futon for my bed in the apartment of 3 NSCAD (Nova Scotia College of Art and Design) girls. Honestly, I had a great time for the month or so I lived there!

Anyway though, I wrote this song while waiting for a ride to pick me up to go somewhere. ANd it just came out. I like the guitar bit, but honestly, it's not one of my favorite songs. My father-in-law seems to like it, so I thought I might post it.

It's another Baha'i influenced song, but I actually wrote the words. I just titled it a few minutes ago, I am thinking... "Desire" but I may change it later.... Nope. It's called "Desire".

Hope you like it.

Get music codes at Bolt.


Not much to say tonight. It's been a loonng week. Things happen. Not good, not great. Just there. Slowly building. Ya. Sounds depressing, maybe it is, maybe it isn't. I have yet to decide. Fatigue brings that on though. On the up-side though... I still move forward. I've had to deal with some fairly heavy issues this past week. One of my views which I found actually seemed to help a situation, which I am not going to elaborate on, don't even ask, I cannot elaborate. Was that the measure of a man is how he (or she) acts when it hits the fan. When everything's going well, everyone loves everyone. There's no reason not to. But when problems arise, that's when the foundation of what makes a person are tested. If that person does what is right, regardless of the consequences (or perceived consequences, case pending), you pass. If you run, hide, get defensive, shut down and enter denial, blame everyone else, others learn volumes about you and what makes you you. Do you accept what's right, or fight it because you think you are right, gets blurry here I agree. But such is life.

It gets messy when the area is gray though, I acknowledge that. While I know it's not right to measure others by your own personal standards, as your own standards may be too low (or high), when you are forced to... it gets tricky. Again, don't ask. I guess the best you can do, is try to find an external reference point (trianulation analogy, or Einstein's Theory of Relativity.... you need an external reference point to locate a specific point, it's more complex obviously, but the idea's there!). And thus brings us back to the beginning of this post... Damn, a circular argument. I am now fallicious. Ah well, my blog, my fallicy. So, to see the true measure of a man, examine him under pressure (external stimuli?). Enough.

A music review now:

Antony and the Johnsons. You may ask who are they, and if you don't know, you have been missing out on some beautiful piano based music with one of the most original voices you're likely ever to hear. The instant you hear a song sung by Antony, you will never forget his voice. It's similar to Billy Talent or The Cure, in that the voice is his alone. And it's beautiful.. Regular readers may be wondering why I only review groups that I think are great... Well, I don't get paid for this, so I'm not going to waste my time writing about songs that I don't like.

But Antony and the Johnsons produce beautiful music. It's on the slow side (not bad slow, good slow), there's no guitar (maybe a little), alot of string arrangements (subtley diffused throughout, not overpowering), and the focus is on Antony's voice with the piano as back up. Some of the songs you really need to just sit back, close your eyes and just listen. I have the "I am a bird now" cd, and I am doing just that with the first track, "Hope there's someone." I can type with my eyes closed exceptionally well now. It's beautiful.

It's getting late and I want to go to bed, so my last bit of advice: Do yourself a favor and listen to them.

Friday, September 22, 2006


So, what's this you ask? This is the problem my lap-top had yesterday. It was missing or corrupt.
Let's add context for my non-existent new readership...

I am a PhD student who is writing up the past 3 or so years of work, which I have submitted my own blood, sweat, years off my life through stress, and very close one day, but not quite because I am a man, tears. Right now, my working existance is on my laptop. Only a really good lottery win could ease my stress if it got stolen.

So, I turn on my computer yesterday morning, go have a shower, come back, and it is cycling through booting and crashing. Sorry if you've heard this before (Phil) but my life is kind of dull and boring right now... So, I try several things, starting in Safe Mode, Safe with command mode only, and a few other little tricks (1.5 hrs worth or so). All of which resulted in a crash before the Windows logo even comes up. So, now I'm shitting myself. Apologize for the swear, but really, can you blame me.

So, I call the company where I bought it from (still under warrantee!!!! Yay for me). The guy tells me to try this, I do, but then it shuts itself off before anything can happen. Let it cool down a bit because it might be overheating.... Try again, same result. Nothing

Not happy Jan. Not happy at all.

I guess the good news about the whole thing is that I did learn how to fix it, and now I have a nice "new" laptop. If you ever have this problem:

Drop your XP setup CD into the drive, press F2 to enter setup when you turn your computer on. Go over the "Boot" heading and move CD-ROM drive to the top of the list (use "+" and"-" buttons). Then re-start your system. Your computer will now boot from the CD drive.

When the XP setup CD starts, and asks you what you want to do, press "R" for repair. Then it'll analyze your system and fix the problem.

Now, if you've been good, like Sir Richard Branson, and have just give about 10.2 billion dollars to combat global warming, you may get lucky and this'll work. Now what did that guy standing next to me say when the guy at the tech shop finishing doing justthis..... ummmm

"That doesn't look good."

And no, it wasn't. The solution for all those who may eventually get a corrupt of missing vgaoem.fon, format your hard. Reinstall Windows from scratch. This'll work. And it did.

So, yesterday, my laptop was re-formatted, erasing every little last trace of everything that I had done. But because I am ultra paranoid of this type of problem. I always have back-ups. So fortunately, nothing was lost. Except ALOT of music I had saved on my computer. I bought a 40Gb Toshiba Gigabeat MP3 player a little while ago, and this acts as a portable hard drive. This has all my music on it, unfortunately it's stuck there as you can't pass it back to a computer (a bit crap, but I'm over it), but it has all of my files, twice, as I make it a habit of keeping 2 separate back-ups from different dates... Just in case....

I also hide this MP3 player at night when I'm sleeping so that it doesn't get stolen if we are robbed. And it's always close to me so that if there's a fire, I can grab it on my manly way to get wife and child out of the house. Paranoid??? Ya, but would't you be? And now I'm glad I'm so paranoid. Yesterday could have really hurt me. Really bad.

But as it is, my lap top runs like new, and is set up properly to actually take advantage of the hyperthreading ability on my 3.0GHz Pentium 4 processor. It's heaps faster now. THanks guy at Pioneer Computers Australia, Thanks....

God had a test for Jesus and the devil. They had 2 write a 10,000 word essay on ... ummm... I don't know, how about: Whether 'tis nobler in the mind to suffer the slings and arrows, or to seek vengeance on those inflicting said slings and arrows until they stop slinging and repent. So, Jesus and the devil sit down to each's computer and write frantically for whichever side they chose. Fire streaming from the fingers of the devil with each key-stroke sounding like a thousand hounds from hell praising his cunning, and surprisingly well reasoned, arguments, and in the crowd, hell's populace cheering(?) him on. On the other side, sat Jesus, and as He typed, a blindingly, captivatingly beautiful light enshrouded him such that all but said hounds of hell could not help but gravitate towards. With the sound of each of His each key strokes echoing the beauty and melodious music that only God's chosen angels could have performed, and even then, only under the strict tutilage and guidance of God, Jesus continued to type. With 5 minutes left though, the fire from the devil's fingers causes a power short and Windows crashed in less than the blink of an eye, leaving both Jesus and the devil staring at a blank screen, reeling at how could this happen with 5 minutes left. Being pretty powerful beings though, they get things up and running with about 1 minute left. Jesus presses a few buttons, including "Print" and then hands his essay in to God, leaving the devil gobsmacked at how Jesus could have produced a 10,000 word essay, and print it in under a minute after loosing everything in the crash!!! The devil mounts a vicious protest citing foul play and cheating with his arms flailing, tail smacking his hounds, and his eyes and skin redder than the most reddist thing you've ever seen times 3 (he's the devil, he hates losing, what do you expect?), but he is instantly silenced by 2 words uttered from an unknown angel in the crowd, "Jesus saves."

Monday, September 18, 2006

The problem with plungers

Alright then, 2 posts kind of in 1 day.. I have been meaning to get this up for a little while, but I have been busy....

This is my boy Alex, as Optimus Prime. The cool thing is that he is now starting to like Transformers!!! Yay for me!! I loved Transformers as a kid, and I have been grooming him to like them as well. He has a few little ones since he is only 3, and the bigger ones are a bit harder to do... And too expensive! But he loves them. Coincidentally, I bought him a little Optimus Prime that I saw at the grocery store the day before his aunt Kim gave him this costume... So he knew who he was supposed to be!!! And he loves it!!! Yes, he likes Star Wars as well, and me and him have regular light saber battles, he likes to be the baddy though with the red light saber.. Good choice my boy, good choice!!

A little while ago was Father's Day as well. And this is me, waking up and opening my new pair of pants that I got along with a shirt and one of the best (and cheapest) presents I have ever received... It just goes to show that you can get a great gift for under 10 bucks easily!!! I don't have a picture, so I'll have to describe it...

Well, where to begin?

It's brown.

A handle on the side...

You guessed it!! It's an awesome coffee cup with no pictures or anything on it, just brown.

But it's what's inside that counts... I only drink plunger coffee at home now, since my office at work only serves freshly ground Irish Creme coffee (seriously, we love our coffee), an instant coffee has to be really good now... Anyway though, To make a plunger coffee, you usually have to dump some of the coffee into a purpose built plunger thing, wait a couple of minutes, plunge, pour the coffee and season to taste (ie milk and sugar, one level teaspoon though, I weaned myself off 2, to be healthier of course).

So, you ask: "Why are you so lazy so as to be complaining about this 5 minute job. I mean really, what's wrong with you."

Well I'll tell you what's wrong with me (I find it therapeutic to talk to, and about, myself in the third person while carrying on both sides of my own initiated conversations...don't argue, just accept and acquisce).

So, my problem is the couple of minute wait.. because I end up going into the computer room, typing, and loosing track of time, so my steeping coffee gets cold, and I get mad. Yes, I'm sensitive about things...Ask Rebecca about my finger-nail scissor incident tonight...Grrrrrrrrrrr Gr.

This cup though, has a PLUNGER BUILT IN!!!!!!! Awesome eh!! So you dump your coffee grinds in, sugar in, milk in, and then fill with boiling water. Bring the whole cup into the computer room and let it sit next to the laptop!! I no longer forget about it, and when I want it, I simply insert the plunger thingy-ma-bob and plunge away... Then drink of course!!!!

How cool is that!!!!

And how's this for a crap post!!!

Nothing really..

Ever have one of those days where things feel right? Today is mine. Woke up alright, albeit a little cranky after a 3 am finish last night. Don't worry though, that is a regular thing now though. SO I woke up, hung the clothes out on the line in the midst of a beautiful day. Made a coffee, had a bit of all natural yoghurt stuff that I find quite tasty... ANd then began to write. It is here where i learned a secret to getting over writer's block, or how do I start this?

Simple is the answer I found. One word. Write.

That's is. The teacher's in school were right!! Just write. It'll fall in to place, and you can just cut-and-paste to rearrange later.

Still feeling a bit high from the Melbourne Prof's comments on my paper. Last major hurdle mostly done.

Things just feel good today.

Oddly though, I have a fairly (understatement) big night tonight, and one that I should probably feel a little nervous about, but I don't. It'll either work or it won't. Yes Mom, you know what it is, but like Marsha, no details yet. Don't want to jinx things. Anyway though, I should go, luch is awaiting in the microwave, and more writing needs to be done.

Thursday, September 14, 2006


Well, it seems that yesterdays venting session worked!!! I got a response this morning!!! Less than 24h after sending the paper off!!!!!

I must reiterate though, that I was never upset with her. Only the present circumstances surrounding my needs and her availability, which I acknowledge and accept may not be compatable up until now. This was no-one's fault, I was just flustered at the circumstances.

Once I sent the paper off, I had a nervous ball of ... I don't know in my gut which pretty much centered around me hoping that I did not send this world-widedly declared expert-in-the-field the work of a moron (meaning me) who was stabbing at whatever he could to analyze the data, and end up embarrasing myself.. But as my Dad recently mentioned to me, (in other words that I am re-arrangine and making fit to what I want to say) it must be hard for me to be right all the time!!! And while that may not be what he said, or even meant, or even thought that I might twist into meaning, I know that's what he felt!!! ya welll....

So, because I am so ecstatic (spelling?), I am posting her middle paragraph of her response outlining what she thought of my paper:

"The data that you sent and that you have included in the paper is excellent. And you have done a very good job in the analysis. I've attached the file with some comments/suggestions in Track Changes - there is one section which needs a bit more clarification - but overall I think it all makes sense. And I like the Conclusion section which brings it all together in terms of a mechanism of action."

Awesome eh!!!

The only real problem, was that she forgot to attach the file with her comments/suggestions. I honestly expected her to crucify it. But she also appreciated having her name on the paper, and she wouldn't agree to that if she thought the paper was crap. Awesome day for me....

In terms of my thesis, though, it is even more awesome!!! It means that my first methods chapter which deals with the subject of the post from yesterday, contains 2 publications, one in the Journal of Biological Chemistry ( J Biol Chem. 2004 Dec 24;279(52):54002-7. Epub 2004 Oct 13) that link will take you to the abstract, and one will be very likely accepted by Biopolymers (as the lady mentioned above is an editor, no I wasn't playing politics with this, coincidences do happen). My second results chapter already has 2 publications, one is Bioconjugate Chemistry (Bioconjug Chem. 2005 Nov-Dec;16(6):1556-63) and one in BBA (Biochim Biophys Acta. 2006 Aug;1763(8):879-88. Epub 2006 May 10). My 3rd results chapter is a method development chapter, so no possible publication out of that.

That's 4 publications in good journals my friends. A good haul for a PhD student!! That also means that the people reviewing my thesis can not say anything bad, as my work is already peer-reviewed and published in international journal, ready to be cited by others!!!

Yay for me!!!

I should get back to writing said thesis though, you still don't pass if you don't submit though.


To open this post, you will understand very little. But I am venting, and vent I will...

Well, I did it. I sent this paper away to a lady in Melbourne who has been very difficult to keep in contact with. I have been working on this paper for over a year now, and I am tired of it. It have slaved countless days, nights, weeks etc trying to analyze the data from two different techniques (surface plasmon resonance (SPR) and circular dichroism (CD), the later of which the picture represents idealized data). We started with a collaboration with a local university around where I live (no train ride, ya for me), but they offered me an honour's student to do the work, and he knew less than I did (of which I didn't know anything about CD.

So he did the work, the pictures looked like shit. For a complete lack of better word, it fits. And the analysis was similar. Sooo, I wrote a program myself entitled PEPFIT Analysis which runs in Excel (Visual Basic) and does the work for you, and is based on another free to use program called PEPFIT which is a pain in the ass to use, and runs in DOS!! What runs in DOS!!! Good program, but runs in DOS!!! I describe this program in a little more detail in my science ref site, greatly named: Another (Not So) Wasted Effort, which bascially puts a few of my bookmarks on the web and acts as a centre for when I analyze gene array data etc.

The picture above is a sample CD spec. This procedure tells you what your protein or peptide's secondary structure may be, with each line representing a different structure. It just shoots polarized light through a sample at different wavelengths (~190nm to ~260nm) and the solution rotates the light left or right, and that's what you see. The more "right" the light is rotated, the more positive the line on the graph goes, and the more "left" the light is rotated, the more negative the line goes. Each strucutre (alpha helix, beta sheet, etc) rotates the light in a particular way at each wavelength, thus the different lines for different structures or conformations. Also, primary structure is simply the amino acid sequence of a protein, and the secondary structure describes what said protein or peptide ... umm.. "looks like", is round like a girl's rignlet (alpha helix) or does it look like corrugated cardboard (beta sheet). That's a great analogy, if I get the opportunity to teach this topic, that's the analogy I will use.. It's perfect!!!


I ended up going and doing all the CD work myself, modified the procedures, and got some beautiful results of which were easily analyzed by my program. Cool, CD bit was done.

Then came the SPR part. I have some beautiful pictures (YES I KNOW I'M A GEEK, I can think of a series of graphs as genuinely beautiful). But I could not analyze them for anything!!!! SOOO many nights till 3 am, trying out other programs like "Clamp"from the University of Utah. And then asking for help from a lady from Melbourne who is probably the best in the world at this, and who has worked with us before, and is a friend of our dept. So I e-mailed her on May 11 (2006). I heard back from her... on July 30 (she has a reputation for e-mailing right back, within 24hrs, except for this time). 2 Months. she asked for a few things, so I sent them to her, the next day or so.

and I am still waiting.

I ended up figuring a way to analyze the graphs myself, by diving into the guts of the analysis. I hate kinetics. It's one of those things where you either "see" it or you don't. I think that I am the later. ALthough, my ego leads me think that if I actually quit resisting it, I would be good at it as I love numbers, and considered it a good exam if I learned something while writing it, Even University Calculus. I don't know, I can always get numbers to make sense. So maybe I will stop resisting and learn some. And maybe not. ANyway though, I did a kinetic analysis, spent the past 2 and a half days finishing the paper and associated figures, and then sent it off to the lovely lady in Melbourne. Hers and one of her student's names are on the paper as they did send me something useful, so maybe I will get a response before I submit...

Disclaimer: I really do like this woman though, she is genuinely nice, and always helpful, and pleasant. I can't honestly say anything bad about her. SHe has had a busy year, office moves, overseas conferences etc.... I'm just frustrated by the time lag. Probably because I am running out...

I swear that I can go on forever, again,
Please let me know that my one bad day will end.
(Blink 182, I'm Lost Without You)

Wednesday, September 13, 2006

Inspired by...

Well I was reading one of G's posts, and notived that she uploaded some music that I think she played and sang... I can not say for sure as when I tried to listen, I realized why I hate dial-up internet.... Too bloody long.. and yes, if Alex was here, he would have told me that that's a naughty word. And he's right, but he can't read yet, so let me re-iterate: dial-up is bloody bloody bloody bloody bloody (breathe in) bloody bloody slow.

Anyway though, I thought that I would try my hand at Bolt to upload something of my own! Soooo it's below. I wrote this awhile ago, it's a Baha'i prayer which I really like, put to music of my own creation. A while ago, I bought a multi-track recorder over e-bay, and this is one of my first attempts with it. I coupled it to N-track on my laptop to mix it and do all that stuff. But for those who are interested (Tammy maybe) It's got 2 acoustic guitar tracks, a bass track, 2 lead vocal tracks to provide a chorus effect and maybe 2 vocal harmony tracks because the best voice to harmonize with is always your own. Anyway, I played and wrote the whole thing and mixed it on the train to and from work over many days. I hope you enjoy it, and if you don't, keep it to yourself. I'm sensitive. And I was taught that if you can't say anything nice, don't say anything at all. Bloody is allowed though because I am still Canadian and it's not a bad word there. A happy day for loopholes.

As for music, I've had this cd for a while, it's Blink 182's last release which contains "I miss you". This cd is rapidly climbing my most listened to cd. It's soo much better than their early stuff, they have shown (or showed as they are no longer a band) heaps of growth to put this album together and there's even a song with Robert Smith! the lead singer from the Cure (another band which you should all know). The whole cd is great though. It's a great mix of great music. Well worth a listen, or many listens as the case may be. But as a disclaimer, I do not promote free downloading music, as it is illegal.

Anyway, I should run, a paper to send to people....

The name though, the song is called "O God, My God" aptly named after the 1st 4 words of the prayer itself. The words have been put to music by other Baha'i's with different music, and I think it was "Innvocation", great title I thought....

Anyway though, enjoy...

Upload music at Bolt.

Sunday, September 10, 2006

Happy Birthday Bec!!!

Well, the other day (Friday, the 8th of September to be exact), my lovely and beautiful and pregnant wife Bec had a birthday. She just turned ......... 21 :) (see I can be sensitive). So we invited her sister's family who have recently returned from an extended stay in Cyprus over for supper, and coincidentally, it was also Bec's sister's birthday too!! Ya, I know, crazy eh, but it gets worse... Bec was born on Sept 8, her sister was also born on Sept 8, but 3 years ealier, and their grandmother was also born on Sept 8, albeit a few years earlier than both of them, and then a few years before their mother was born. So, Sept 8 is a big day for the family!

Anyway though, so they all came over for a supper, and a chocolate cake that Bec had made. It was a nice evening, Alex loves his cousins heaps and was really happy to see them... A story I may tell tomorrow if you're all lucky, or more importantly, if I feel up to writing...

But anyway, I thought I would post another video of us singing happy birthday to Bec for her ... 21st.

Monday, September 04, 2006

"He died doing what he loved best."

Honestly, I have several things I would like to say that's been going on in my life, but they are petty. And genuine tragedy has occured today, not just for Australia, but for people, as well as animals across this great planet. You all know, so I won't be giving details, read one of many articles if you haven't watched it on tv yet.

He was a champion for all animals, big, small, pretty, ugly, friendly, and unfriendly. I remember the first time I saw his show "Crocodile Hunter." It was super late at night when I was in my first year of University at Carlton (In Ottawa Canada) and me and Emily were watching tv, and this came on and she was like "You HAVE to watch this guy, he cracks me up. He's crazy!" So we did, and ya, she was right. But he was soo captivating, and energetic. I think what drew people to him was his devotion to his cause. Everything he did had a single minded focus, protect wildlife, of any form. And he would use whatever media he could to further it. Not himself, but the cause he stood for.

A sad day indeed.

And by a ray, a bloody big ray, but a ray.... Such a passive creature to be responsible for such global sorrow.

When I heard, I was on my way to my citizenship ceremony and I thought that I would look at the news on my cell phone, and there it said, "Crocodile Hunter Steve Irwin dies." Then both me and my phone froze. Me out of shock and saddness.... Stopped mid-stride as I tried to grasp this.... I don't know what to call it.... this moment in time. my phone felt it too because it stopped working as well, I couldn't get it to open the actual story for about 10 minutes... So I was wondering what happened, hoping it wasn't a crocodile that caused his untimely end. But, he died doing what he loved best.

My heart, hopes, and prayers go to his family (wife Terry and 2 children, "Bob" and Bindi). And may the legacy of the legend that is Steve Irwin live on until the term "endangered species" has itself been wiped out.

I became an official Australian citizen tonight.

Of this, I am proud. If for no other reason than that I can consider myself a fellow country-man of the late Steve Irwin.

Steve, you will never be forgotten, nor your message lost.

Steve Irwin