A great man passed away today

"Today is truly a sad, sad, day." With these words my father opened his speech at his father's funeral. And today he passed away and the words are just as true today as they were then. My father was a truly the one that held the family together during tough times. He was a wonderful father, and grandfather (and if I can believe my mother a great husband too). But we lose more than just a member of the family. My father was truly a visionary, and he set standards of excellence in teaching, politics, and public speaking that will be nearly impossible to meet. His humanity and the love for his country will remain unrivaled for many years to come. It is hard for me to say more at this point. He will be missed.

The day after

Yesterday was Father's Day. I didn't write a post on Father's Day like I did for Mother's Day. I did call my father and talked to both my parents yesterday. Today he is fighting for his life attached to machines to help him breathe. The prognosis is not good. He is still relatively young, at 62, he is too young to die in my opinion. He is a vibrant, witty, eloquent, incredibly smart and outspoken man. Quite a forceful human being. Actually that just about sums him up: "human being." His philosophy of "live and let live" is one I've always aspired to copy. A biologist himself, he instilled in me my love for biology. His outspoken atheism has always allowed me to see the ridiculousness of prayer and believe in imaginary friends. His ideas about politics are always way too progressive to fit comfortably in this day and age. His relaxed attitude in the most severe crises could calm down the entire family. Who will take charge now that the family is in crisis and he is at the center of it?

It is so painful to be apart from my father, mother, aunts and cousins, when I want to be with them, now more than ever. It would take me about three days to get home, and it does not sound hopeful that he will make it that long. And then there are a lot of other issues that I'm not entirely comfortable discussing on this blog, that would make it indeed very, very tough to return to the States afterwards. Going to be with that part of the family may mean being separated from this part of my family indefinitely. The unfairness of this situation is infuriating.

I'm hoping he will pull through and see F1-3 at least once.

Aching backs, necks and heads

I hope they supply free Aleve at the entrance to this church.

And Ibuprofen here.

and ibuprofen here.

Small victory?

Earlier this week, while waiting for F1-2 to finish his therapy session, I talked to another parent who was doing the same. He told me he was considering discontinuing immunization of his son. I talked to him for almost half an hour, and I think I've convinced that's not a good idea. If he is concerned about his son getting so many at the time, he can always spread out the immunizations. He and his wife seem like very dedicated parents to me, so they don't mind going back to the doctor more often to give their son all his shots. I had some help from another parent too, so I cannot take all the credit for this. It is good to know that he will make the best choice for his kid and protect him and others around him from some very serious diseases.

Update

In case anyone was wondering.... I am still alive. I just have several projects going on that sadly take priority over blogging.
1. Write a report on microarray analysis.
2. Keep current lab experiments going.
3. Work on construction project at home.
4. Schedule and prepare for a committee meeting.

In addition, P1 and I have signed up for a research project with to assist our communication efforts with F1-2. This will be quite intensive, with meetings twice a week, and activities every day.

Don't worry, I will be back.

New species found in tropical rainforest

[Photograph by Paul Ouboter]

From the website of Conservation International, this report of 24 new species found in Suriname, South America.

A number of insects, especially ants were found. I suppose it's easy to see how ants can be overlooked. They are rather tiny, the forest is rather thick, and Suriname must be ant paradise. But there were also some reptiles, like the frog with fluorescent purple markings and small fish.

The study was the result of a collaboration between Conservation International and the two bauxite mining companies in Suriname, Suralco and Billiton Maatschappij. About 80% of Suriname is covered with rainforest, and the bauxite industry is its single largest source of income (70% of export earnings).


[Source: nl.wikipedia]

Suriname's tropical rainforest is at risk as a result of logging result of mining activities.

Cell identity

Ok, back to the basics. I need another break from raw data.

I've briefly discussed the basics of DNA and RNA in previous posts. I've also introduced transcription. So what's the big deal? As it turns out, although every cell in an organism has the same DNA, different tissues, have different genes expressed at a given time, resulting in their unique characteristics. So that is why a plant leaf looks different from a flower a root. Whether a gene is expressed (turned on) or not (turned off) depends on available transcription factors. The availability of these transcription factors again depends on whether the genes encoding these transcription factors are turned on and so on. As you can see it can get rather complicated.

In general there are different levels of regulation in the pathway from DNA to final product. This list is not intended to be complete, but should give an idea of what can happen.

1. Transcriptional regulation (is the gene turned on or off?)
2. Transcript processing orpost-transcriptional regulation (changes to the transcript can affect subsequent steps)
3. Translational regulation (is protein made from the available RNA?)
4. Post-translational regulation (sugars or lipids can be attached to proteins)

Protein activity is regulated on a number is different levels, which warrants an entire post, so we'll leave that for another time. For the purposes of this discussion, it is enough to know that different cell express different genes at any time.

Now that we know that, we can ask: so which genes are turned on/off in this cell, but not in that. This is also referred to as "differential expression." And in a nutshell, that is what microarrays do. For the entire genome in one single experiment (with more controls than experimental treatments, but that is the nature of the beast).

Differential expression will be covered in a future post (hopefully soon).