18 December 2013
My new website… in case anyone is still coming here… ever.
www.lucentstardesign.com
This is an online portfolio I have just recently created for my graphics & artistic works. Feel free to take a peek.
Now I know, this has nothing to do with Australia considering I'm back in the US and I haven't posted anything in forever, but I just wanted to get some links out there.
Thanks for looking!
~Ta! :)
P.S. in case it wasn't listed here, Del also has a website for his lab at Wilkes University:
www.lucentlab.org
I designed that website for him as well, so have a poke around there if you're interested also.
09 June 2010
What's a blog!?!
So, we've been doing okay here... keeping busy and such. We did make a short trip out to Great Ocean Road, but since we got a late start, we didn't make it very far. Oh and when you see a sign about not feeding birds... DON'T!!! It's just bad... I don't remember if my camera was working then, but if it was, I'll try to get some of those pics together as well. Otherwise, Del and I have just been enjoying each other's company.
Once I've gotten some motivation back, I'll actually post the Healesville blog, I just have to uncover the patience to wait for stuff to load and think of how to actually speak again. I've gotten used to only talking in short statements and not really speaking coherently as of late. So anyway, that's it. Maybe you'll hear from us again sooner lol. Thanks for checking in!
~Cheers
05 April 2010
What Del is working on in Oz (part 2)

Onto the third question: "What is computational modeling?" I assure you it is not laptops walking down runways with fashion photographers shooting pictures (although some may argue that is exactly what Apple's product launches are becoming...). In general computational modeling involves using a computer to represent the physical properties of an object or process. There are computer models for all sorts of things: how aerodynamic your car is, how a rocket will behave when leaving orbit, how the climate changes, and in my case, how proteins do the things they do. The movie you saw in my last post of a protein folding is an example of computer modeling (or computer simulation, I like that term better). Computer simulation is frequently used to study molecules (and proteins in particular). This is because computers can do certain things easily that are more difficult to do in reality. One example is mutating a protein. It is trivial for a computer to make a number of mutations (changing one amino acid into another), while to do this in the real world requires a lot of expensive lab equipment. Another thing computers can do very well (when it comes to looking at proteins) is to watch the movement of specific atoms on very short timescales. Small rapid changes in a protein's shape can be modeled very easily in a computer where to observe them in reality requires some very fancy equipment (i.e. temperature jump spectroscopy).
In addition to these sorts of things there is one place where computers really shine: doing repetitive tasks very efficiently. Humans on the other hand aren't so great at this. If an experiment needs to be performed 100 or 1000 or more times, it is difficult to find a young scientist who can do this in a timely and reproducible manner. Usually robots and special techniques are employed, which as you can imagine costs lots of money. Computers on the other hand specialize in these repetitive tasks. Computer scientists call these tasks "embarrassingly parallel" or "trivially parallel" (I prefer the phrase "pleasingly parallel", but that's just me). To put this in real world terms, ditch digging would be an embarrassingly parallel problem. If you need to dig a ditch that is 100 feet long, it may take one guy 24 hours to do it. But what if you get 2 guys (who both work at the same pace)... it now takes 12 hours. By this logic, it is very conceivable that you can get 10 guys and have the ditch dug in about 2 and a half hours. Of course there is a limit to this, after which you can't parallelize the problem anymore (you can't dig the ditch in one second with 86,400 people).

Now onto the last question "What is directed evolution?" Directed evolution is essentially making evolution do what you tell it, or evolving things in the laboratory for a specific purpose. To understand this I'll briefly explain how evolution works. You already know that your genes (your DNA) encodes the instructions to make all of the proteins in your body. What I haven't told you is that over time, genes can build up mutations wherein something (radiation, chemicals, viruses, natural replication) makes a small change to your DNA (mutagenesis). This results in a change to your protein. Sometimes these changes don't really show up or have any obvious effect at all (silent mutations). Other times they can have a drastic effect on an organism (either good or bad). If a bunch of organisms have to compete for limited resources, nature will select for mutations that make an organism more fit to obtain those resources. That organism in turn has a higher rate of survival and passes its genes on to its offspring. Of course because all organisms are evolving and their survival affects each other, this results in a complex and constantly changing evolutionary landscape. I've drawn a little picture below of this concept using bacteria as an example (which also illustrates how natural selection leads to antibiotic resistant bacteria).

An interesting example of evolution can be found in the case of sickle-cell anemia in sub-Saharan Africa. One small change of one amino acid in hemoglobin causes it to loose much of its ability to do its job (carry oxygen around your body; it's also what makes your blood red). You would think that because of this, people with sickle-cell anemia would all die and the trait would disappear. It turns out that genetics are a little more complicated than that. Because we get one set of genes from our mom and one set of genes from our dad, a person can end up with both a normal hemoglobin gene and a sickle-cell hemoglobin gene (this is called a heterozygote, and can be considered 'carrier' of a gene). Now here's where it gets really cool. It turns out that people with one bad gene and one good gene are resistant to malaria (a deadly blood parasite transmitted by mosquito bites). So people with 2 good genes (dominant homozygote) have a higher chance of dying from malaria. People with 2 bad genes (recessive homozygote) have a higher chance of dying from sickle-cell anemia. But people with a good gene and a bad gene are resistant to malaria yet still have enough good hemoglobin to survive the sickle cell disease. Thus you have an evolutionary niche where the mutant gene has a good chance of survival. Here is a picture I put together illustrating this example:

- allow us to create an enzyme that is designed to be really good at breaking down pesticides
- learn something about how good we are at designing enzymes and hopefully find ways to improve
31 March 2010
What is Del working on in Oz? (part 1)
The task of my post-doctoral fellowship is to design biocatalysts using combined computational modeling and directed evolution. I have other projects here as well, but this is the job I was hired to do. This is all well and interesting since a. I have never done this before, and b. this has only been done successfully a handful of times…ever. So it will be challenging and when I succeed you can all say “Good job Del!” or when I fail you can say “It’s okay Del you did your best, anyway it was a really hard problem!” and behind my back you can whisper “Dumbass went all the way to Australia to tackle an impossible problem and he couldn’t pull it off…how lame!” Now you may be asking what he hell “to design biocatalysts using combined computational modeling and directed evolution “ even means. It is for those of you asking this question that I’m writing this post. I’ll try to answer the most obvious questions over two blog posts:
- What is a biocatalyst?
- Why do I want to design them?
- What is computer modeling?
- What is directed evolution?
Okay let’s get started. Question 1: What is a biocatalyst? Well, it is an enzyme. Enzymes are a type of molecule that performs chemical reactions in your body. These reactions include breaking down your food, passing signals around your body, making your blood clot, making your toenails grow, and a whole mess of other things. You need enzymes because the chemical reactions your body needs to survive don’t happen at the right speed for them to be useful. For example you eat glucose (sugar) and you get energy to do your tasks. Your body oxidizes glucose to carbon dioxide, which you breath out, and in the process you get some energy, which is used to keep you alive and healthy. Your body uses enzymes to do this. You can oxidize glucose to carbon dioxide without the aid of enzymes. Just get some sugar and leave it exposed to air. Wait for it… nothing happens? Well using oxygen to oxidize sugar happens very slowly. We need to add something to speed things up. Well, what if we burn the sugar? That works, but most of the energy goes away as heat and we can’t use it for anything. This is the same problem your body faces. You need to extract the heat from burning glucose and use that to do other jobs. Enzymes make this possible: they act as catalysts for your body’s chemical reactions.
How do they do it you may ask? Well before I answer that question I’m going to give you all a basic biology lesson about what an enzyme is made of and inevitably what you are made of. The answer for the most part is protein. Enzymes are made of protein, or rather enzymes are proteins. Though not all proteins are enzymes. Proteins are the basic mechanical building blocks of nearly all life (this could be debated for viruses but we won’t talk about that now). Also, they perform nearly all tasks that are involved with maintaining life.
So what does a protein look like? For starters they are very small. Only the biggest proteins can just barely be seen with the most powerful microscopes. More specifically they range in sizes from say 1 nanometer to 10 nanometers. But they can join together to make structures that are much bigger (these are the ones that can be barely resolved by the most powerful microscopes). By the way, one nanometer is 1 billionth of a meter. So if you can take the smallest mark on your ruler (1 millimeter) and divide it into a million equal parts, they will each be 1 nanometer in size. So proteins are really tiny. How do we see them then? Well it turns out that the reason we can’t see them is that the light we use to see is actually larger than the protein (the wavelength of visible light is longer than the dimensions of the protein). So we need a very special camera that takes pictures with much smaller (shorter wavelength) light: x-rays. To see a protein we need the high energy x-rays that come off of particles whipping around almost as fast as the speed of light in big rings called particle accelerators. My boss is an expert in using these high-energy xrays and some very special cameras and computer programs to figure out what proteins look like. Here are some pictures of smaller proteins compared against Rhinovirus AKA “The Common Cold” (whose coat is made of protein).
This picture was cropped from a great poster available at the RCSB (http://www.rcsb.org). Click to zoom in so you can read the names if you're interested.
Now, the next question is how does your body make proteins? This is actually one of the fundamental concepts of biology. So fundamental in fact that they give it a really stupid name: “The Central Dogma of Molecular Biology”. I will explain the central dogma using a factory as an example.
In the boss’s office (nucleus of the cell) there are sets of blueprints (your DNA) on how to make all of the different things a factory can make (your proteins). The blueprints don’t ever leave the boss’s office, so we need to make copies so the assembly line can go to work. So we make a photocopy (the process of transcription) of the blueprint and this photocopy (mRNA) is what the assembly line will use. Now the photocopy is read by the assembly line (the process of translation) and the end product is made (protein). The assembly line is actually a big (well big compared to proteins) device called the ribosome. Below is a picture of this process (DNA and mRNA and final protein not drawn to scale sorry!).
When the ribosome makes a protein, it assembles it from basic building blocks called amino acids. These amino acids are attached end to end like differently colored beads on a string and your DNA determines the order in which they are attached. But this string of beads needs to fold up to make a functional protein. This magical act of self-assembly is called protein folding (and is what I studied under Vijay Pande while at Stanford University). This YouTube video shows a computer simulation of a protein folding (this is from work done by a number of talented lab-mates of mine and published in http://pubs.acs.org/doi/abs/10.1021/ja9090353). Note that this movie uses a different representation of the protein than the previous pictures. The arrows and coils are meant to show what shape the "string" is in while the balls and sticks are meant to show what shape the "beads" are in.
So, let’s summarize. We know that enzymes are proteins that do chemical reactions in such a way as to make them useful to our body. We also know that proteins are assembled from amino acids like beads on a string according to instructions written into our DNA. We know that these proteins are very small, but can do all sorts of tasks in your cells (some of them actually even look like larger real world objects such as scissors, salad tongs, camera lenses, etc). And we know that these proteins fold up into the correct shape in order to do their job (imagine how cool it would be if you could just attach all of the parts of a car end to end and then have them magically fold up into a functioning automobile…just goes to show what crazy and amazing things happen on the scale of really small things like the cells in your body!)
Let there be macaroni pictures
So, there are a ton of pics (not kidding). They show the various stages our apartment has gone through, from no furniture to what we have now. We could still use more, but gotta save a little money before we can do that. If you want to stick it out all the way through, I hope you enjoy them, if not, I'll put text in between each segment of pics so you can pick and choose your place to look by watching for the bold texts. Each picture can be enlarged by clicking on it and some of them have some flavour text added for your viewing pleasure. So here you go, I'll shut up with the random thoughts now and move on to the more desired content:
Del is giving the tour:



























Ta!
02 March 2010
Random Thoughts
(starts with the American - then the Australian equivalent)
*Ground Beef - Mince Beef (this comes in 1 through 4 stars, premium and quality - don't know the real difference between 4 star and premium or quality) - NEWLY ADDED forgot this one before
*Rice Krispies - Rice Bubbles
*Raisin Bran - Sultana Bran (raisins = sultanas here, you won't find ANYTHING that says raisin)
*Tomato Sauce - Tomato Paste (regardless of texture) (tomato is pronounced Toe-Mah-Toe)
*Ketchup - Tomato Sauce (nothing says ketchup, not even Heinz)
*Meat Sauce - only says Bolognese (I didn't know what that was until 2 years ago - freakin' lame!)
*Scallions - Spring Onions
*Peppers - Capsicums (red and green)
*Ounces and Pounds - Metrics (duh hahaha)
*Shopping Cart - Trolley (people look at you like you're crazy if you say cart)
*There is no Pudding!!! Only Dairy Dessert!!! (and VERY limited in brand and flavors)
*Eggs are NEVER refrigerated in markets... they're always on a shelf near baking goods
*Fly-bys - these are not like savings cards, they give you "miles/Kilometres" toward flights (you still have to apply for a card at every store that offers them when you go)
*Who knows what a yellow squash is!?!? They don't have them here!!!
*Candy - Confectionery
*Fresh Dog Food is sold right next to the human meat (and I mean no separator)
*American Cheese - Tasty Cheese
*Cheddar Cheese - Tasty Cheese
*Aged Cheese/Sharp Cheese - Extra Tasty (this means extra nasty - in my humble opinion, but really look for the fine print "aged for extra flavor" or "aged for extra tastiness")
*Mac & Cheese here really SUCKS and there is no Velveeta
*There are no M&Ms!!!
*There is no Chef Boyardee, just fake substitutes that either use, regular tomato based sauce on their pasta, or a tomato cheese sauce. No Meatballs! No Ravioli! Nothing like that at all.. no Spaghetti O's either... no variety
*You can get baked beans in a cheesy tomato sauce or just a tomato sauce (no variety)
*Aquafresh - Macleans
*There is no Crest! (I can't find it anyway)
*Mascara cost in US $6-$12 for a drugstore brand - Mascara cost in AU $16-$27 for drug store brand (that includes CoverGirl)
*Light Bulbs - Globes
*Biscuits - Bikkies (like cookies, not the dinner sort - they're also not sweet, like Stella Dora)
*Cheer! - Dynamo (laundry detergent)
*Snuggle - Huggle
*Downy - Fluffy
*Clothespins - Pegs
*No Tums! Only Mylanta
*Claratin - Claratyne
*Tylenol - Panadol (with Paracetamol 500mg)
*Drug labels are also very different here, in the states, anything the FDA regulates is specially laid out on the package, there is nothing like that here, sometimes you really have to search for the fine print to find out what is in something (i.e. panadol, deodorant, hand sanitizer, etc)
*Nicorette - Nicodyne (haha, I saw an add for that one)
**For the ladies - Boys skip ahead**
*no applicators! unless you look for the one brand that has them (everything like OB)
*liners are 98% of the time scented
*haven't really found any of the "cure" stuff yet, but luckily, don't need it ;P
*no Midol!
*Make-up - prices through the roof! (for drugstore brands - $20 lipgloss, $25 foundation or powder)
**Ok, it's safe now!**
*There are no Swiffers!
*Paper towels rolls are hard to find
*Removed for censorship purposes.... haha you snooze you lose!
*Veggies need to be extra washed when you purchase them fresh... I've found dirt and bugs in mine after getting them home (ick!!!!)
*Most foods are pretty bland when you purchase them, most sweets aren't that sweet unless it's confectionery and almost all food needs some spices added (and a lot - even when dining out)
*Campbell's Chunky Soups - Heinz Big N' Chunky Soup
Okay, I'm done boring you with my random blob of thoughts. It's just those have been in my mind for some time, so I thought you'd enjoy! And just so you know, I'm not complaining about these things (except the mac&cheese thing), I find them interesting (interesting enough to share). It's crazy all the little differences you find, not even the big ones, it's just the little ones that really stand out! Well, now you know some for whenever you decide to travel here! ;P
Ta!

26 February 2010
Canberra - The Capital Territory

Here is the Old Parliament Building:

Within the Parliament Building (new of course) you can find an original copy of the Magna Carta:

On the first day there, Del and I tried to walk to Parliament together, but got slightly off track and ended up walking around the giant man-made lake and ended up at the Australia National Museum (as mentioned in my previous post). This place was pretty neat looking, here is a view from the top of the Parliament Building (notice the Chinese Embassy in the foreground):





I know you're all looking forward to pics of the apartment, but I haven't worked on them yet. Shame on me! I know, but the truth is, I'm still trying to decide if I should show pics of the 1. empty apartment, 2. partially furnished apartment, or if I should just wait until we have 3. a little furniture (like a couch)... so if you'd like to make suggestions for me as to what you would like to see, please comment here so I can decide more quickly as for what to post. Ta!