What Dave writes

Advice is seldom welcome; and those who want it the most, always like it the least – Lord Chesterfield 1748 in a letter to his son.

Have you ever felt compelled to give someone advice or to advise them of their mistake when you know that they have erred but hesitated to do so? I know I have, on many occasions. For example, you may notice an apparent and undesirable bad habit that a friend has. Most if not all times, I would like to tell them about it and I have many times in the past. Sometimes they tell me “Yeah I know, it’s something I’ve been trying to adjust”. But after a while when you meet your friend again, they don’t seem to have changed at all. Other times people like to justify their bad habits or they tell me it’s really not much of a big deal. And at that particular moment, I don’t really have anything to say. For once I would like someone tell me “Oh sorry I hadn’t noticed, thanks for telling me” upon hearing my advice. But most people are aware of their problems, they just sweep it under the carpet and it resurfaces every now and then.

So over the years, I’ve lost enthusiasm towards giving people advice. If people want to change, they will do it themselves. More importantly people don’t like it when you’re not minding your own business. But as a friend to the many people who have problems, I still want to tell my friends how having such a habit is bad for them. Sure I have many bad and poor habits myself (who doesn’t?) and I’m not a qualified psychologist/counsellor of some sort. But I still would like to tell them.

On the contrary, I would love to have someone tell me of my problems. I would appreciate the effort of them telling me of my problems. But most people don’t like to talk about these things to avoid awkward conversations. And I have to admit I’m not the most inviting person when it comes to conversations, so I have yet met someone who has told me of my problems (or perhaps I’m just perfect). It would be nice to have someone come and tell me of a bad habit that I have; for example “Hey Dave, you know that yawning without covering your mouse is pretty rude in Australia?”. I have been told that once when I first came to Australia, and have since never yawned without covering my mouth.

When I look back on all these worries I remember the story of the old man who said on his deathbed that he had had a lot of trouble in his life, most of which had never happened — Sir Winston Churchill

I love reading articles that I can totally related to and understand. Today I read this one titled “Self Doubt: A Disease that Doesn’t Discriminate!”. The article starts off much in the style of “The Eighth Habit” by Stephen Covey, where the author writes about common problems everyday people faced. I could relate to many of the listed issues related to self doubt; “What if I’m not qualified enough?”, “What if I get all excited – like I always do – and then fail?”, “What if I disappoint people?” which ultimately leads to “Hmm, perhaps I need a little more time to plan and think about this”.

The only thing I wanted to add to the article is that fear is such a deeply embedded disease. And even when we have acknowledged our problem of fear and made a decision to face our fears, it is an extremely difficult problem to face. Rejection and humiliation are the worst feelings in the world, which is why fear is so powerful. So while the article was great, I felt it was a little tough on people whose lives are affected by fear. I whole heartedly agree that the solution is you, because only you can face your fears and manage your fears. And it’s one of those problems that takes so much effort to correct but the tiniest set back can undo all that was done. The solution I believe will involve a lot of support from friends and family, and taking very small steps on the stairway of fearlessness.

The seven myths about sleep.

Sleep is the watering place of the soul to which it hastens at night to drink at the sources of life.
In sleep we receive confirmation … that we must go on living.
Abram Tertz (Russian writer and dissident)

It is no secret that sleep plays such as important part in our lives. However there are many (including me) that choose to neglect sleep. Whether they want to get more work done, believe that sleep is a waste of time or just stay up for the heck of it, sleep is pretty low priority. The article I included at the top of this post explains some of the seven myths about sleep.

The gist of the article is really this: we need 8 hours of sleep, no more and no less. Sleep too much or too little, we will develop the same problems. While there have been some very successful figures that functioned on less than 8 hours of sleep per day, it is not ideal. Additionally, in the article I got an interesting perspective on catching up on sleep. Although I find it hard to sleep in on the weekends, due to my circadian rhythm, some people can and like to sleep in over the weekend. I remembered hearing from a source that we can “store” sleep, so sleeping in on the weekends either provides us with a sleeping buffer over the weekdays or we can recharge our lack of sleep. And while this may be true, this will utimately upset our circadian rhythm and normal sleeping pattern which I never really thought about.

The other myths covered were about medication and chronic sleeping problems, which I don’t think I have. If you suffer from chronic insomnia, see a physician. If sleeping problems come sparingly take medication or sleeping pills. And tylenol PM is not a better alternative than a prescription drug.

While there are many mysterties to sleep, one thing is for sure; we all need to sleep. This necessity is the basis of my belief that during sleep our body revitalises and replenishes our bodily supplies, much like a gardener watering the plant that is our soul.

Admiration is a very short-lived passion that immediately decays upon growing familiar with its object, unless it be still fed with fresh discoveries, and kept alive by a perpetual succession of miracles rising into view – Joseph Addison (English essayist, poet, playwright and statesman).

I’ve had some experience as a salesman and one of the things we were trained on is impulse. Always remember to remind the customer that this is a limited offer (even if it isn’t). Impulse is also the basis of those infomercials you see 3am in the morning (if you’re ever up watching t.v. at that hour). Call now and receive this and that absolutely free. This offer is only limited to the next 500 callers so be quick. I’ve been suckered into buying one of these products. It was a series of audio cassettes that claims to help your memory. The first couple of tapes were pretty cool, but eventually I found the product to be pretty shallow and unapplicable. I was 14.

We are constantly trying to distinguish between admiration or passion, lust or love, and impulse or real need. We try to change careers, change partners, buy new products all in an attempt to find our passion. Why is it so hard to find something that we can adhere to? I believe it has to do with freshness. The quote at the start of this entry basically encapsulates my whole belief of passion. I believe humans are innately wired to keep demanding freshness. It’s a trait that has been selected during evolution. Because if we were content with what we had, the human race wouldn’t have evolved so quickly since the neanderthals. No other species are like humans, which you may argue is not a good thing (listen to Agent Smith in “The Matrix”).

So unless there is a perpetual succession of freshness, we won’t really further lust into love, admiration into passion and impulse into continual need. It’s just like playing a role playing computer game, where you want to level up your character and find the best items in the game. But the addiction dies out once you have reached the highest level and found all the items in the game (which is something I have achieved in Diablo 2, twice). I had my level 99 character (with several others close to 99) and all the best items in the game; then I asked myself now what?

So when you are searching for your passion, find something that continually brings you joy and a feeling of accomplishment (Diablo 2 is probably not an ideal candidate). Find something that makes you get out of bed every morning (preferably not coco pops). And once you find your passion, I’m sure great things will happen.

“You’re free to speculate as you wish about the philosophical and allegorical meaning of the film — and such speculation is one indication that it has succeeded in gripping the audience at a deep level — but I don’t want to spell out a verbal road map for 2001 that every viewer will feel obligated to pursue or else fear he’s missed the point.” – Stanley Kubrick

I just finished watching 2001 A Space Odyssey, and as always the first thing I do after seeing a movie is to visit its wikipedia page to read the plot and interpretations of the movie. Even for movies that weren’t meant to be particularly deep, I always read up. The quote by Kubrick was given when asked for an interpretation of 2001. By and large, I totally agree. Since we are all different, we all pursue our own intellectual thoughts.

So the question on my mind is what was this monolithic block? One of the reasons I always read up on a movie is because I’m afraid I missed the point, which Kubrick pointed out. I’m afraid to make connections, which differ from the director/author’s intentions. But just like how Tarantino has his interpretations on the song “Like a virgin” (which perhaps wasn’t the song writer’s original intentions), shouldn’t we all have our interpretations on things? Maybe this is why 2001 is highly acclaimed.

As for what I got out of the movie, I guess it was the special effects. For a film made in 1968, it is pretty spectacular. The “Dawn of man” was particularly boring for me (and I kept thinking back at The Simpsons awesome parody of it) and the lack of dialogue and prolonged cinematic effects didn’t do it for me. I loved the HAL 9000 portion of the movie, and finally understood all The Simpsons references made to it. The only thing gripping about the movie was the monolithic block, and trying to figure out what it is. I’m truly a mystery fan boy, with favourites such as The Maltese Falcon and Chinatown.

The block will remain an enigma, just like the intentions of the movie. My overall interpretation of the movie? Computers will eventually get smart enough and take over us (which it has probably achieved already on my part, since I spend a crazy amount of time in front of a computer).

Saturday night 11:30pm. What better way to spend time than writing random facts about cancer.

Q. What is the relationship between telomeres and cancer?
A. Increased telomerase activity can increase longevity of cells, but it is also implicated in cancer formation. Almost 90% of cancer cells have been found to have enhanced activity, and a cancer cell usually divides about 80 times before a tumour mass becomes large enough to be detected In contrast, normal human cells usually divide 30 to 50 times before telomeres become too short and doubling stops.

Q. Who was the first individual to find the gene for breast cancer?
A. Mary Claire King (1946-) determined that in 5 to 10% of those women with breast cancer, the cancer is the result of a mutation of a gene on chromosome 17, the BRCA1 (Breast Cancer 1). The BRCA1 gene is a tumour suppressor gene and is also linked to ovarian cancer. Subsequently, other researchers were able to clone the gene and pinpoint its exact location on chromosome 17.

Q. What is an example of a drug developed through pharmacogenomics that is associated with cancer?
A. Gleevec (approved by the FDA in 2001) is a drug developed for a rare type of genetically caused chronic myeloid leukemia. In this type of leukemia, pieces of two different chromosomes break off and reattach on the opposite chromosome, causing a chromosome translocation. This abnormality causes a gene for a blood cell enzyme to continually manufacture the enzyme, resulting in high levels of white blood cells in the bone marrow and blood. Gleevec was specifically engineered to inhibit the enzyme created by the translocation mutation and to thus block the rapid growth of white blood cells.

Recently I posted a question to the Perl beginner mailing list about Perl and bioinformatics. My question was asking why Perl is better than other scripting languages when it comes to working with text. And as a final note in my email, I made a remark towards to how parsing text is useful to biology since a lot of biological data is stored in text files.

I had an abundance of answers (some that I am still slowly digesting), and there were several reasons towards Perl’s superiority in text processing. In no particular order, here were some answers to why Perl is good/great at text parsing:

1. Regexes are first class citizens in Perl, in other languages you must use a library that feels out of place
2. Perl tends to innovate in regexes, adding features (the most popular non-Perl regex library is PCRE, PCRE stands for Perl Compatible Regular Expressions)
3. Perl is weakly typed, which reduces the amount of code you must write. In strongly typed languages you spend a lot of time casting variables into the desired type.
4. Many of the operators like the readline operator (<>) are setup to do what you want with a minimum level of effort, such as a bare readline operator creating the default UNIX filter style (read from stdin if no files are specified on the commandline, otherwise open each file passed on the commandline and read from each of them in turn).
5. The, much maligned, set of special variables also makes this easy (for instance, $ARGV is set to the file currently being read by the construct in the last point).
6. Perl’s regexes are still better and faster than the compatible libraries. There are many things Perl can do that they can’t even come close to (my favourite is the /e modifier on s///!).
7. CPAN is another major reason for Perl’s strength in text processing. There are hundreds if not thousands of modules that parse, mung, generate text in all sorts of forms. just consider how many templaters there are alone.
8. Perl’s scalar values are designed from the start to be powerful text storage items. they have no fixed limit on size, you can add, cut, shrink, extract, etc directly with operators instead of long winded function calls. the Perl ops and functions are designed to work well together generating concise (a better word and more accurate than terse) code. Perl’s guts have been optimized over many years and are very fast when doing text munging.

So from what I have gathered Perl’s regexes give the user power to create complex text parsing abilities and since Perl’s scalar values can be limitless in size, large chucks of text can be stored and operated upon. It also seems that the special variables and operators available to Perl make it easier to work with text and pattern matching.

And after some further discussion with a Perl guru, I understood the concept of type casting and how Perl’s many operators assist with writing less code for casting variables. They also mentioned about strongly typed languages like C++ where 10.0 + 5 would result in an error due to addition between a floating point type vs integer type. This was also touched on briefly in the “How Perl Saved The Human Genome Project” and how weak casting can be a problem if a variable changes from a number to a character. This often happens as a lot of data is manually handled and human errors do occur.

And just today I corresponded with a fellow bioinformatician who has used Perl for almost 10 years. They wanted to point out that biological data isn’t just huge genomic files (which makes Perl extremely useful) and as such other scripting languages are just as competent as Perl, which was also a note made by another Perl guru. Apparently Ruby is extremely popular in Japan, and was developed by the Japanese. There is even a BioRuby! But the point is really that for many bioinformatic tasks such as parsing XML files, Perl holds no advantage over other scripting languages. Perl is just popular in bioinformatics because it was there first.

It has been a very insightful thread and I did get a lot out of it. It helped me understand the history of Perl and biology and bioinformatics, and explain why Perl is very suitable in parsing large text files. However I have heard that Perl’s syntax is hard to read and ugly. I guess when you’re developing software, readability plays a large part. Besides Perl is known to be quick and dirty and considered to be the Swiss army chainsaw. But hopefully when I get my python bioinformatics book, I can get a better perspective.

Viewing some of my monthly subscription videos for National Geographic on YouTube, I came across a special edition National Geographic video of Dr. Michael Wesch of Kansas State University, titled “The Future of Communication”. It captured my attention from the start as he was describing his experience in Papua New Guinea. The region in PNG that he studied was extremely isolated even more so than Bougainville, the place where I grew up. It was up in the highlands and he stayed in huts without electricity. But during a 10 year period he was able to witness a transformation in PNG. This transformation occurred with the introduction of writing, leading him to understand the relationship between media and relationships; media mediate relationships and when media changes so does relationships.

Dr. Wesch studies anthropology, which is the social science that studies the origins and social relationships of human beings. With his observation of how media can alter society and social relationships, he started to study the new media landscape called Web 2.0. In short Web 2.0 is web development that focuses on two things; users and information sharing. YouTube, wikipedia, blogs, flickr, digg are just some examples of Web 2.0 applications that allow you to share videos, knowledge, information, photos and articles respectively. As more people become connected to the internet and networks become faster and more ubiquitous, Web 2.0 applications will only get more popular.

Understanding how this new media landscape will impact society will help us rethink our outdated ideas, for example current teaching methods, which is Dr. Wesch’s interest. It was while lecturing that he noticed how current teaching methods were not suitable for today’s generation. I have not seen the other videos on his class projects but basically the projects have focused on combining the knowledge of every single student in his class. This new interactivity has let in a breath of fresh air in his classes and achieved impressing results. For his innovation teaching techniques he was awarded U.S. professor of the year in 2008.

The video has made me think about the future of communication and how it will shape everyone’s lives. And to help myself understand I have made delicious, digg and twitter accounts. I can see the definite trends in today’s society; open source software, free knowledge, applications that allow human interactivity, increased connectivity and faster network connections. If a collection of 200 undergraduates can develop ground breaking research, imagine the power of combining the minds of the world. The most popular sites on the web are the ones promoting interactivity; facebook, myspace, wikipedia, file sharing sites, etc. The most popular games are MMORPGs such as WoW. I think Dr. Wesch was right on the future, we will only see an increase in interactivity and faster connections to the internet, which will allow everyone to be connected to everyone instantly. Good or bad? No idea but it will definitely be very interesting.

Today (6th August) I gave blood; it was my first time ever and at the start of it I was a little anxious. I don’t like needles; I can usually handle pain fairly well but there’s just something about needles I don’t like. Nonetheless I made the first step towards doing something worthwhile.

It happened very randomly; I was walking to get some candy and the next minute I decided to go and give blood (and I didn’t even get to the lolly shop). We actually talked about giving blood over dinner a couple of nights ago and I guess it got to me. I walked to the van and approached the friendly staff, two of which were psychology students studying the blood giving experience for first time donors. Usually people make appointments, but it just so happened that there was one last time spot at 3:30pm, which was the time then.

As I thought I would only be out for a little while getting candy, I didn’t bring a jacket. So while waiting I was suffering the consequences and hence shivering, which could be from a combination of my anxiety and chilliness although at that time I thought it was probably just the weather. I filled in the paperwork and the pre donation questionnaire, which I offered to participate in, and there was a bunch of questions asking about how I was feeling. I have to say I was feeling a little more negative than usual.

Once it was my turn I walked in van. I got pricked for a haemoglobin test and the result was good; I had a reading of 165, which is quite high according to the nurse. My blood pressure was also good; 121 / 71, so physically I wasn’t stressed. Then came the moment of truth. I jumped on the bed and laid out my left arm trying not to think about the needle. I avoided looking at the needle, and in an instant there was a quick sting and that was it; it was in me. I don’t remember much discomfort as I was happily passing out my fluids. It ended in about 10-15 minutes and was given a popper, cheese, crackers and chocolate. I had to wait 15 minutes before they let me go so I used it to fill the post donation questionnaire.

It had the same questions, but this time around when I was filling out the form I felt much more positive. I felt more confident, more at ease and happy. It is somewhat like the feeling you get after finishing an exam. The feelings experienced were quite different before and after the blood donation. There was also a feeling of righteousness and peace. I know giving blood isn’t so much of a big deal but you can’t help feeling like a better person. I have already made an appointment for next time and I know this time round it won’t be as negative.

I have recently read a post from zen habits about “being still”. It described today’s society as one that is in constant motion; one where we spend each moment doing something or another. A busy lifestyle is seen as one that is productive and engaging; on the contrary when we are being idle or still we are percieved as being lazy or inefficient. As a consequence we try to jam pack as much as we can in a day; when we get a spare moment we’ll check our emails, our phones or read up on news. We feel the need to constantly bombard ourselves with information so that we seem to make the most out of 24 hour day.

However while we might be achieving more, there is a price to pay. In the exact words of Leo (founder of zen habits) “This comes at a cost: we lose that time for contemplation, for observing and listening. We lose peace.” Life is all about balance, and we can’t neglect the part of us that requires this peace. With that I decided to be still for a moment and reflect.

I sat and pondered on my current situation. I looked back 4 years ago, a fresh honours graduate going through a tough relationship. I suffered from depression, low self esteem, and a general lack of direction. It was tough back then, especially when I lacked the support I needed. It is a very long story (which I plan to graduately write about), but I am glad to have met many people along the way that made things better. Life is very different these days. I’m in more control of my life and much happier. I still have the down times but they don’t last. I have chosen to be happy.

Thinking back and reflecting makes me appreciate the things I have today. I enjoy my work, I am in good health and have a better half. Sometimes it is nice to be still; it makes you appreciate the things you have in life.