Monday, April 30, 2007

Intelligent Design

Finally! Intelligent Design explained. HT to Bronze Dog.


This year (2007) has been declared the Year of the Dolphin by the United Nations, and the United Nations Environment Programme.

Sadly, another gruesome video today. This link is one sent to me a while ago, and is one of the reasons I wanted to start my own blog. It is most definitely not for the weak of heart! I do not entirely agree with the commentary at the end of the video that blames the Japanese government exclusively for this cruelty to dolphins. The consumers are also to blame. The public is allowing it to continue too. In addition, this probably generates a not so insignificant part of their GDP.

Yes, I have been to a slaughterhouse, and yes, I have seen an innocent cow being shot to death, and cut apart for its meat. There is something much more vicious, cruel, and inhumane in this video than that though. The cow I saw getting killed was dead in an instant, and if had not been, he would have been shot a second time. Is it really necessary to let the dolphins bleed and slowly suffocate like that? Is there no better way of doing this?

I was also sent a link with a petition to sign. I did not sign the petition, because I think there is more to this than just blaming the Japanese government, but more than a million people seem to disagree with me and have signed it.
The picture below was created by Erik Christensen; edited by Jack Rockley, and taken from:

Harpoon and drive hunts are not limited to Japan. This picture was taken on the Faroe Islands.


During transcription a gene encoded in the DNA of an organism is read by and a strand of RNA is made based on the DNA template. This is much like the DNA replication process, with the difference that only one strand of RNA is formed in transcription, and the nucleotides are ribonucleotides. During replication, both strands of DNA are copied and the copies are also DNA, made up of deoxyribonucleotides.

Because a DNA molecule has many genes on it, how does the transcription machinery know where to start and where to stop? Within the DNA sequences there are signals encoded that help the transcription machinery find the right spots. These are called the upstream (just in front of the gene) and downstream (just after the gene) regions. The stretch of DNA immediately upstream of the DNA is often referred to as the "promoter" of the gene.

The DNA "tells" the transcription machinery where to start, with a certain stretch of nucleotides, so that for example (and this actual sequence is totally made up for this purpose) a stretch of nucleotides "AGCTAGCCGACAT" means: this is where you should start making RNA. How can that work?

The sequence of DNA that serves as a signal is actually bound by a particular protein that can recognize and bind that sequence and sequences that are very similar to it, but not sequences that are different. The protein that binds this particular stretch of DNA is called a transcription factor and in turn binds other proteins that are transcription factors, which in turn "recruit" RNA polymerase to the complex of DNA-stretch and proteins. Now the RNA polymerase knows where to start and so it does. Once it is a little further down the DNA strand, very busy making mRNA, another polymerase can start at the beginning and making a second strand of mRNA. In this way it is possible that many polymerases are making the same strand of mRNA at any one time.

An example of such a transcription factor is called TBP, which stands for TATA-binding protein. This is a protein which can recognize and bind a sequence of DNA called a TATA-box, or Goldberg-Hogness box. The TATA-box has the sequence "TATAAA" at it's core and a bunch of more variable sequences around it. TBP finds, and binds the TATA-box, then a protein called TFIIA (transcription factor IIA) binds TBP, and then TFIIB and TFIID join in, and RNA Polymerase can now bind these proteins and start transcription.

The stretch of DNA that is recognized by a transcription factor is called a cis-element, while the proteins that bind cis-elements are called trans-factors.

At the end of the gene there are again signals encoded in the DNA sequence that tell RNA polymerase it is time to stop, because the end of the gene has been reached. This is called the transcriptional terminator. There are two ways in which transcriptional terminators work. One is called Rho-dependent transcriptional termination, and depends on the presence of a particular protein called the Rho factor to stop transcription. The second is called intrinsic transcriptional terminator. This is really cool, because the signal is a palindromic sequence at the end of the gene, that can fold over and bind tightly to itself, forming a hairpin structure.
It looks something like this:

Credit for this picture:

Research or teaching? Here or there?

What do you want to be when you grow up? Good question. I, for one, don't really know. I've been a graduate student for so long, I'm not sure I can do anything else. I'm very good at being a student....

After I got my undergraduate degree I worked in the middle of nowhere for a couple of years. It was fun while it lasted, but lack of conversation with anyone above middle school level, tends to dumb you down after a while, and I was craving discussions at a slightly higher intellectual level.

Then I moved to the States to start my graduate studies, and it was definitely heaven after my previous stint. Lots and lots of really smart people to talk to. Now I've been doing that for a long time. I changed programs somewhere along the line, and I'm quite happy where I am, my adviser is absolutely the best. But what will I do when I graduate?

There was a time when I thought I would always want to be on the cutting edge of science. I envisioned myself doing research for the rest of my life. Now I'm not so sure anymore. I love doing research, but research doesn't seem to love me back. I seem to be missing the necessary ingredient of luck, and probably some other stuff as well.

There might be an option to stay in my current lab if my adviser finds funding for a post-doc. It seems he would be happy to have me if he does find the funding. After that I could at least in theory keep myself funded if I write my own grants.

Research does tend to take you away from your family an awful lot though, and since I've managed to accumulate 3 kids since I got my BS, my priorities have shifted. I'd prefer to spend my weekends hanging out with my hubby and kids instead of shedding sweat, blood and tears in the lab. I think I might prefer to teach when I'm done. I realize that the pay would be significantly less, but money isn't everything. getting hired in a predominantly teaching position might be a bit of a problem too, since my program is mainly focused on research, and the teaching requirements are limited to a single credit of "teaching assistant," which translates in preparation for the labs of the course. That's not good enough in terms of accumulating teaching credentials. I try to teach guest lectures whenever possible, but that's not impressive either.

And then there is the question of location. Where will we end up? For legal reasons it might be easier to stick around here. However, job opportunities are fairly limited, especially for teaching. Immigration issues might cause problems and force us to look elsewhere. Canada is an option, but it's too cold for me. My beloved husband says that British Columbia is a great place to live and the weather isn't that bad. According to my mother-in-law and brother-in-law (who live in Canada) job opportunities in the Vancouver area would be limited too, and they would highly recommend Toronto.

I guess I have another year or so, and then I'm scheduled to finally graduate. We'll see what happens.

Vaccinate your children

When F1-2 was tentatively diagnosed with autism 4 years ago, I encountered the argument that mercury in vaccines was a contributing factor (in addition to the argument that gluten/casein sensitivities were). I read articles, surfed the web, contacted the local autism center and got more information. I decided that there was no evidence that mercury had anything to do with autism. And even if there was just the minutest of changes, the risks involved in not properly immunizing my child were much, much greater. I went ahead and F1-2 received all his immunizations as scheduled. F1-3 was born 3 years later, and received all of hers too. Here is a painful reminder of what life was like before there were immunizations. This is *not* for the weak of heart. Yes, as with any medical procedures there are risks involved in having your child vaccinated. However, autism is not one of them. And the benefits far, far outweigh the risks. In addition, every child that is not immunized out there, increases the risk of new outbreaks. Scary, scary stuff.

Blogging in the nude?

Apparently today is blogging-in-the-nude day. Ok, so what? How is that different from any other day?

Saturday, April 28, 2007

Finished project

Well, I had some setbacks, and it took me a little while to put up this post after I had finished but her it is. Project for the month of April.

P1 and I had decided that getting a swing set for the kids was a great way to spend our tax return. That's not as simple as it sounds. First, we had to borrow a pick up truck from a friend to go pick it up. Paying for it was painful, these things don't come cheap!

I spent an entire evening unpacking the two large boxes and carefully sorting, measuring, and labeling all the parts. Of course, it never fails. Several parts were missing. I had to call the manufacturer to send replacement parts. The parts took a week to get here, but luckily they were necessary for some of the later steps of the construction, so I could get started anyway.

P1 is the nicest, and at least to me, the most exciting guy in the world, but anything more complicated than changing a light bulb is not for him, so the construction project rested solely on my shoulders. In addition he is so busy this semester, that I was not counting on his help holding parts up during assembly either.

So, gradually I started putting the pieces together. All the lumber was stacked up in neat piles on our back porch with the labels attached. I could only work on it on the evenings after the kids went to bed, and even then not for very long. One morning, about a week after the project started I went out to the porch, and found that F1-3 had carefully removed all the labels from the lumber, and placed them on the coffee table in a neat little pile. She ran to stand next to it and was obviously very proud of her handywork, and wanted to be praised for her hard work.

It took me a few days before I could muster up the energy to start re-labeling. And even then, I caught F1-3 on a few occasions, trying to sneak by to remove some of the labels. Finally, I finished both sides of the fort, and it was time to attach them to each other with the lumber for the front and the back. I could no longer go on by myself. F1-1 was spending the weekend with his biological father, P1 was too busy preparing lectures, what to do? Luckily, one of F1-1's friends stopped by looking for him, and got cornered into helping me out. It got dark shortly after he arrived, so I could only attach the front of the fort. The whole thing looked rather unstable, so I leaned it against the house, hoping that would provide enough support. And it did. At least, as long as it was just standing there.

A few days later, I decided to try and attach the back, hoping it would be more secure once I had done that. When I started, the whole structure came crashing down. I guess it wasn't that stable after all. Two pieces of lumber were damaged. I had to wait until it was Monday to call up the manufacturer again. They were very nice about it, and said they would sent the replacement right away. It took 5 days before that got here.

A week or so later, when F1-1 was with us for the weekend, I enlisted him and his friend to help out. This is not easy. Tell your pre-tween: hold it up straight, and pay attention. Keep holding it up straight. Yeah, right! Like that's going to happen. Oh well, eventually, I managed to get to the point where I could tell the guys they were off the hook. and from then on it was pretty steady going. And the end result is not bad......

Monday, April 23, 2007

The theory of evolution

Today I showed a colleague my blog, and he noticed my post on "Darwin-related activities". He asked me if I believe in Darwin's theory of evolution. To say I was surprised by this question would be an understatement. The way he phrased it and the tone in his voice, made me turn around to look at him. With his interests in phylogenetics and systematics, surely he stares evolution in the face every day!

The closer look at his face confirmed my suspicion. Uh oh. My colleague is not convinced evolution is real.

We could not talk for very long, I still had stuff to finish up in the lab and I had to leave to pick up the kids 20 minutes later, but we talked briefly.

I explained that in my opinion "believe" is the wrong word to use with regard to a scientific term like "evolution." I accept evolution as the best explanation of both the diversification of and similarities between species, until a better theory comes along.

Scientists come up with theories. Based on those theories they formulate hypotheses that can be tested by doing experiments. They do the experiments, collect data, analyze the results, which either support their hypothesis or don't. If they don't, they formulate another hypothesis and the cycle starts all over. The accumulation of experimental data and results as published in reputable, peer-reviewed journals forms the basis of how widely accepted a theory becomes.

The theory of evolution has withstood thousands, and thousands of papers published over many years, all of which have ultimately supported the theory. Or more accurately, to the best of my knowledge, no publication exists with evidence that is incompatible with the theory of evolution*. That would have forced scientists back to the drawing table. If there was evidence that clearly disputed the theory of evolution, there would be an army of scientists on it right now.

After talking with my colleague for a few more minutes it became clear that he is aware of different proposed mechanisms for evolution. Scientists agree that evolution is a result of accumulation of mutations, with different ideas about the nitty gritty details of the mechanisms of speciation. How fast, what causes different rates of evolution. It is possible that his indecision lies there, with the mechanisms of evolution, instead of evolution itself.

Well, I suppose we'll continue the discussion, hopefully tomorrow. I'm curious to find out more about his opinion.

*Note: Bible quotes do not constitute evidence.

Friday, April 20, 2007

Darwin-related activities

Since yesterday was the 125th anniversary of Charles Robert Darwin's death, it seemed appropriate to attend a screening of "Flock of Dodos."

Let me start by saying it was indeed quite funny, and it was very clear at the end who the real dodos were. But I thought that was part of the problem. If the idea was to sway people who are on the brink of realizing that Intelligent Design (ID) is just disguised creationism, it might fail. I suppose it depends on who the target audience is. If they are those who already think that ID does form a scientific alternative to evolution, the film is just preaching to the choir.

The major ID proponents are painted as a small, misguided group of science-affiliated people (I cannot bring myself to say scientists) and the filmmaker does make fun of them. However Randy Olson could have done a better job of very briefly have evolutionary scientists explain why some of the main arguments of ID don't make sense. Only once did someone mention that the human heart is not perfectly designed. And no evolutionist addressed the imperfect design of the human eye, and the wide variety of eyes that currently exist in nature. Irreducible complexity was also not effectively countered; no one addressed that eyes are indeed not irreducible complex, and that neither are bacterial flagella. A statement by member of the Kansas board of education that there are no (or not enough) transitional fossils was left unchallenged.

At the same time, evolutionary scientists (8 distinguished ones at the poker table) did not do a very good job of making their arguments clear. They came across as a bunch or arrogant clique-ish men, unwilling to step down from their pedestals and explain to the lowly masses why ID is gibberish.

The Discovery Institute refused the filmmaker access to their opulent premises, which made them look very silly. Also, individual ID proponents were more than willing to state that in their opinion the intelligent designer is god, which wasn't very smart on their part.

In the end neither side was portrayed particularly flattering. In theory, I agree that ID is nonsense, but if you want to convince people that it has no place in science class, you need to do a better job of showing *why* ID does not belong there, as opposed to simply portraying proponents as ID-iots.

Sunday, April 15, 2007

Atheist rights

With thanks to Hank Fox and John Wilkins for starting and editing the Atheist Declaration of Rights.

I also agree with John Pieret's comment on John Wilkin's blog that "equal time" may be hard to calculate/enforce. Does every kind of religion get "equal time?" That can get very messy.

Katylava's comment on Hank Fox's blog about being able to establish tax-exempt organizations to promote secular values is covered in paragraph 4.

So, I would take out the first sentence of paragraph #3, start the next sentence with "The nonreligious" instead of "They."

Nonreligious Declaration of Rights

1. Freedom from Fear and Hate:
In every part of a secular society, the nonreligious have the right to live free of fear for their personal safety, their homes, pets and possessions. The nonreligious have the right to be safe from public hate speech and vilification.

2. Freedom of Speech:
The nonreligious have the right to freely speak of atheism in public, or to publicly display characteristic messages or symbols, without fear of repercussion, in the same degree that religious speakers enjoy.

3. Equal Time:
The nonreligious have the right to equal time with religious voices on any public issue. They The nonreligious have the right to equal and open airing of their convictions, views and concerns, and to participate in any public discussion of morality, ethics or social issues, to the exact degree that religious voices are invited to speak. The nonreligious have the right to equal time to respond, on any stage or medium, anytime non-religiousness is covered in a negative light. The nonreligious have the right to equal access to media in order to weigh in on science, medicine, social policy, political campaigns, etc., and to receive respect equal to that given religious voices.

4. Equal Rights:
The nonreligious have equal rights in the work environment, in voting, in running for public office, in serving on juries or any other public or social/civic duty. The nonreligious have the right to be free from religious discrimination in the seeking of housing or jobs.

The nonreligious have the right to join any civic or educational organization that people of religion can join, without discrimination.

Nonreligious organizations have the right to public resources, information or publicity on an equal basis with religious groups. Nonreligious organizations aimed at good works have a right to the same sort of tax advantages that religious organizations have.

The nonreligious have the right to decline to take part in religious ceremonies, and to refuse religious oaths, without fear of reprisal or disenfranchisement. Nonreligious soldiers have the right to claim conscientious objector status on an equal footing with those of any religious persuasion.

5. Equal Representation:
The nonreligious have the right as taxpayers to know that tax money intended for public works and charities is not diverted to bolster the coffers or support the sectarian message of any church or religious group. The nonreligious have the right to government free of religious influence, schools free of religious coercion, and courthouses free of religious oaths.

6. Religious Freedom:
The nonreligious, like all citizens, have the right to be free of religious proselytizing in captive public environments such as schools, courthouses, and public sporting events.

All people, including minor teens, have the right to express religious preferences – including atheism – different from any historic religious tradition without fear of reprisal from family, social or political group, tribe, church, or government.

7. Family Integrity:
Nonreligious parents have the right to expect that their children will be safe from harassment and prejudice when away from home. They have the right to expect that their children will not be singled out for ridicule or aggressive religious proselytizing.

The nonreligious and their children have the right to freedom from religious proselytizing, baptizing, involuntary conversion practices or invasive medical procedures in any venue such as hospitals, emergency medical or senior care facilities.

The nonreligious have the right to NOT have their words or deeds rewritten after their deaths through stories of deathbed conversions.

8. Scientific Integrity:
The nonreligious, like all citizens, have the right to expect that publicly-funded scientific research is carried out by scientific principles rather than religious ones, and that medical research and decisions should be informed by science and reason rather than religion.

Friday, April 13, 2007

Not recommended reading

With three kids (four, if you count P1, my husband), and being a full-time graduate student, I don't get much chance to read. Most of the reading I get to do is by listening to books on tape. Right now I'm listening to what is supposed to be a SciFi novel "The Second Angel," by Philip Kerr. Sadly it's a lot more Fi than Sci. I'm starting to get really bored by it. More than not being exactly fast-paced, it's the scientific inaccuracies that bother me the most.

Specifically, on tape 1, the author claims that blood provides the most convincing evidence of intelligent design. Because several proteins are required for blood to transport and deliver oxygen to the cells, the author concludes that blood is irreducibly complex, and the chance of blood having occured by "accident" very, very, very small. Conclusion: god did it. Sigh... How creationists go from A to B to C is a mystery to me. Nothing can account for this but faith, certainly nothing having to do with education, intelligence or common sense.

On tape 2, the author explains the genetic background of Thalassemia, which is a blood disease caused by a recessive gene. The author botches the description, stating that the parents of an infected child both had to be homozygous for the gene (of course that would make them very sick, instead of just carriers of the disease). He also explains to the shocked parents who had no idea that they were carriers of a genetic disease because no genetic screening is done in parents in the mid-21st century, that their background is to blame. The father is of greek descent and the mother of italian descent, and in the Mediterranean Thalassemia is much more prevalent, because it confers some resistance to malaria. Nonsense, of course, to judge from this map. Unless the Mediterranean was relocated to the southern part of Africa or something in the early 21st century, malaria is not particularly prevalent there.

So now I'm at the end of tape 2. I wonder whether to continue reading this book and to post my commentary here, or to just give up and not waste any time reading nonsense. It may be fiction, but with such egregious errors, there is not a lot of fun it. Ok, that's it. I'm returning this piece of junk and getting something good instead. Maybe something from Kurt Vonnegut (who is up in heaven) to counteract the bad taste left in my mouth by Philip Kerr.

Update: Ok, book was swapped. If anyone can think of any reason why I should go back to the library and check it out again to finish listening, just let me know.

Tiny steps

Another breakthrough!! This one at the home front. When F1-2 (my second son) was 2 he could shake his head if he meant "no." At some point (we're not exactly sure when), he lost this skill.

Losing skills that children have already acquired is common in children with autism spectrum disorders, or as in F1-2's case, in children with seizures. A year or so ago, the neurologists finally figured out the cocktail of chemicals necessary to halt his visible seizures, although there are still numerous spikes on his EEG, and there will always be. A few months ago we started seeing a few seizures again, and in early March his meds were increased. The seizures prompty stopped, and we haven't seen any seizures since then.

I think it was in November or December 2006, when his speech and occupational therapists, frustrated at F1-2's lack of improvement despite the absence of seizures for 9 months or more, decided to radically change their treatment. Dr. Greenspan's Floortime approach was the method of choice, and the speech therapist actually took a couple of weeks off from F1-2 so that he could use the time to study Floortime. Floortime was developed as an integrated approach to treating children with autism spectrum disorders. Although, in F1-2's case we know there is a physical cause of his sensory integration issues, he is in many ways like children with autism.

At this point I don't know whether it's the lack of seizures, the Floortime approach, or a combination of both (most likely it's the latter), but something seems to be working. We're gradually seeing little steps, little improvements, where there were virtually none for 2 years.

Anyway, back to the main story. This morning, F1-2 was watching his favorite show on tv (he really only watches one, and we have numerous episodes on tape), and a child on the show was shaking his head to indicate "no." And my beloved, wonderful little F1-2 shook his head "no." At first I thought it was a coincidence, but he clearly though it was hilarious and repeated it several times. He also continued to shake his head when he'd had enough of breakfast.

This is significant, because:
1. F1-2 is rarely acknowledges the existence of other human beings, let alone the ones on the tv screen.
2. He does not normally mimic other people.
3. He shook his head within the right context when he did not want to eat any more. This means he understands the true meaning of shaking "no."
4. He was obviously proud at his accomplishments.

For most people shaking "no" is taken for granted, even by parents of young kids. For children with special needs and their parents this is a huge step. I'm bubbling over with pride and hope for my son's future.

Thursday, April 12, 2007

Great news in plant pathology!

This study shows for the first time that a resistance gene product from the plant (in this case the N gene from tobacco) and an elicitor from the plant pathogen (p50 from Tobacco Mosaic Virus [TMV]) physically interact during the plant defense response. This evidence has been illusive so far.

A Novel Role for the TIR Domain in Association with Pathogen-Derived Elicitors Burch-Smith TM, Schiff M, Caplan JL, Tsao J, Czymmek K, et al. PLoS Biology Vol. 5, No. 3, e68 doi:10.1371/journal.pbio.0050068

(Thanks to the Evilutionary Biologist whose link to PLoS I followed to discover this paper).

The N gene from tobacco and other related solanaceous plants confers resistance to the plant host against the plant pathogenic virus TMV (Tobacco Mosaic Virus). An elicitor is a protein that comes from the pathogen, and enters to host cell. Numerous papers have given indirect evidence of elicitors being recognized inside the host cell by plant proteins (often the actual resistance gene products), and setting off signal transduction cascades that result in a resistance response. In plants a resistance response is most often associated by rapid cell death of the host tissue in a localized (small) area. This is called the hypersensitive response, and the theory is that this cell death is a form of apoptosis (programmed cell death) to prevent to plant pathogen from spreading to surrounding tissues.

In many plant host-plant pathogen systems, interaction of a resistance gene product with an elicitor molecule could be shown in the lab (in vitro), but it was never shown in a life plant (in vivo) before. Until now.

One of the TMV elicitors is the p50 protein. The p50 proteins appears to interact physically with the protein encoded by the tobacco resistance gene N. They do so both in the cytoplasm and the nucleus of the host.

The N gene was always suspected of being involved in protein-protein interactions, because of the presence of the LRR domain. The LRR (Leucine Rich Repeat) domain, is found in a many proteins, in many different organisms, and is usually responsible for interacting with other proteins. This paper however, shows that the TIR (Toll-interleukin 1 receptor homology domain ; another part of the N protein) is crucial for the interaction with p50. This domain is named after a receptor molecule found in animals that is involved in innate immunity, a rapid response against pathogen invasion.

In future posts I will explain the background of the research and the basics of plant pathology some more.

It means "STOP"

... and not "I can just squeeze by." I'm talking about the red light on top of the yellow and green ones of the traffic signal.

Recently I was driving by a car accident, when I noticed an acquaintance of mine standing by his wrecked car on the road. I stopped to make sure he was ok, and to see if I could do anything to help. He got hit by a car running the traffic light, confirmed by several witnesses who stayed behind to relate this to the police.

It only takes a few minutes to wait for the next green light. But it takes much longer for the wreckage of your car and yourself to be cleaned up from the road. It doesn't make any sense to run the light. It is not only very rude, but bloody inconvenient for you and the driver you're hitting, not to speak of the danger. Your turn was when the light was green, if it's red, it's someone else's turn. I didn't think that is so tough to understand.


And for a way to keep your bagel intact during transport.... I'm definitely going to try this one out some day. I have several of these things. Saves on garbage too.

Cool toy

Hey, there is this really cool toy that I want to try out. I can write sentences in Hindi, even though I can't speak a single word of the language. I want to play!!

हे, तेरे इस थिस रेअल्ल्य कूल तोय ठाट ई वांट तो त्रय आउट। ई कैन राइट सेंतेंसस इन हिंदी, एवें थौघ ई कैन'त स्पाक अ सिंगल वर्ड ऑफ़ थे लंगुअगे। ई वांट तो प्लय!!

Excellent parenting

Wow!! I'm really blown away here. Excellent parenting skills, really groundbreaking techniques of positive reinforcement. It is wonderful to get close to your kids and talk about what's on their minds, isn't it? Great example of encouraging independent thinking. Thanks to Daniel.

Saturday, April 7, 2007


I suppose I really should start with DNA replication, but since I'm anxious to move on to microarrays and complain, I choose to cover transcription first.

Most people should know by now that every cell in an organism has the same DNA. Numerous tv shows have helped popularize the science that allows a villain to be identified by his/her DNA left on a cup, or on a victim's body. But if all the cells have the exact same genetic information, how does a liver cell become so different than a skin cell, or a brain cell? The answer is RNA.

As I mentioned before, each gene has a start and an end, and takes up a relatively small part of a DNA molecule. Within each cell a certain number of genes are transcribed into RNA, while other are not. The genes that are transcribed can be translated into protein, giving each cell a complement of proteins that determine what kind of cell it is. So a root cell in the plant will have a different set of genes turned on than stem or leaf cells. Genes that are transcribed are said to be turned on, while genes that are not, are said to be turned off. There are genes that are expressed in every cell, no matter what kind of cell it is, and no matter what the developmental stage of the organism is. This is called constitutive expression. At the other end of the spectrum there are genes that are only turned on in one particular cell-type. Most genes lie somewhere in between and are turned on in some, but not in other cell types.

In addition to spatial regulation (some cells but not others), there is also developmental regulation, so that cells change the genes that are turned on or off as a result of development from a young cell/organism to an older one. Genes can be turned on or off in response to environmental cues, like wounding, or a response to pathogens. An important point to make here is that expression levels of genes are not as simple as "on" or "off." For any gene a little more or a little less transcription can have dramatic effects on the cell. Changes in the expression levels of genes are called "differential regulation."

As a result of differential regulation, the RNA in a particular cell can say a lot about the activities that are going on in that particular cell at that particular moment in time. Scientists therefore often want to know which genes are being expressed and what that level of expression is.

In a later post I intend to write a little more about how cells turn genes on and off, and regulate expression levels. For the description of microarrays, it's enough to know that genes are differentially expressed.


Why have cells evolved to have both DNA and RNA? Would it not have been easier to skip the whole RNA step, and go straight from DNA (storage of genetic information) to protein (workers of the cell)? I don't claim to have all the answers, but some aspects are listed below.

1. The RNA world hypothesis proposes that RNA existed before DNA did. RNA can catalyze (help along) some reactions in the cell, a process usually credited to proteins. It looks like at some RNA might have been all that was necessary. Storage of genetic information, and workhorse.

2. Proteins would then have evolved later. With 20 possible amino acids to choose from to form proteins (as opposed to 4 nucleotides in RNA), proteins were more flexible, and could evolve to do the job faster and more accurately. They also evolved to do jobs that RNA was incapable of doing. The allowed for much more possible variation, a big advantage if selection for fitter organisms is necessary.

3. DNA is suggested to have evolved as genetic storage because it is more stable than RNA. The extra oxygen atom on the sugar-phosphate backbone of RNA, makes it more reactive, and therefore less stable than DNA. For storage, DNA is more reliable. Any researcher who has worked with both DNA and RNA can attest to the fact that RNA will degrade much faster than DNA does.

Sleepless night

So much for my relaxing weekend! F1-2 woke up around 2 am, and was making an awful lot of noise in the room. I went in about 3 times to try to tuck him back in and get him to go back to sleep, but to no avail. Every time I went in, he had turned on the light, turned off the lullabies playing on the stereo, and was climbing up on the furniture, or pulling at the closet doors.

It's been a long time since we had such a bad night. His seizure medications are to blame for his insomnia. For the past 9 months it appeared that the insomnia was not as bad, but then the seizures started returning. About a month ago, the neurologist increased the dose of his medication, and voila! The insomnia is back. Sadly this means that at least one parent has to get up too, and often he manages to wake up F1-3 too. F1-2 is non-verbal, so we can't just tell him to go back to sleep. Now of course his sleeping pattern is totally thrown off for the day. He will want to nap for several hours this afternoon, and have trouble going to bed this evening. It's promising to be an interesting weekend.

One good thing though, except for about 15 minutes around 3:30, F1-3 slept through it all, and she is still asleep. I'll have to figure out a way to regulate F1-2's sleep for the day. Wish me luck.

Friday, April 6, 2007

Theocracy and abortion

Reasons for banning abortion are of a religious nature. When legislature makes laws based on religous principles, there's guaranteed to be trouble. Religious dogma is not very well thought out. In this case, numerous lives are ruined as a result of backwards theocratic actions.

In my opinion:
1. Every child should be desired, wanted, and welcome in this world.
2. If the mother wants an abortion, it is a necessary procedure.

As a mother of three myself this hits close to home. Why would legislature have anything to say about whether or not I can have an abortion? The mother is the one to have to carry the child. She is deprived of income for having to take time off to have the baby. She needs to buy diapers, feed the child, get up in the night, take care of a sick child, take it in to the doctor, take it to school. She needs to purchase clothing, pay for daycare, schooling, and deal with puberty.

What is the point of having an unwanted child who is going to grow up miserable? Anti-abortionists protest loudly if a mother wants to have an abortion, but what are they willing to do once the child is born? Suddenly the child's life is worth a lot less. No one is willing to pick up medical costs, especially ap roblem if the child has special needs. When the child was born to a drug-addicted mother, chances of this are even higher.

Paying a mother $500 not to have an abortion, is of course madness. The $500 does not even cover her cost for food during pregnancy. This bribe would appeal very much to drug-addicts, resulting in even more kids born with challenges.

A few months ago, I met a teenager whose mother was a drug-addict, so he was placed with his grandmother after numerous foster homes failed. He was mistreated in a number of the foster homes. I met him after he had been placed with his grandmother. It was very obvious that the grandmother was addicted to drugs (crack cocaine maybe?). She hit the kid, yelled at him, curse at him, and was paranoid. If he so much as looked at her, she started yelling that he was stealing from her, and that he hit her. She did not think it was necessary for him to go to school. The poor kid. He seemed to be a good enough kid, but how can you possibly turn out right having to live in an environment like that. A few days after I met him, he was sent back to his mother. I wonder what his life is like now.

There are so many children alive right now who need our help. The world is already overpopulated, why don't we take better care of the children that are already born, instead of trying to increase the number of unwanted children that we simply cannot take care of?

Theocracy is the cause of suffering of many children who otherwise might have been aborted. Sometimes is better to have no life at all, than to have to live in the cruel world.


I get to do research on Friday morning!!

Woohoo! I may actually get to do real research this Friday morning (that is, if I stop blogging). My F1-2's therapy sessions have both been cancelled for the day. Don't get me wrong. I know how important his therapy is, and the therapists have gone out of their way to make it as convenient as possible by scheduling him early in the morning. However, the sessions do take an enormous chunk out of my mornings twice a week. But not today. I can get the kids ready in the next 15 minutes and head out of here, drop them off, and be on my way to the lab. My PI will not believe his eyes when he actually sees me there before 8! This is promising to be a good and productive day. I hope yours is too. Or not, if you're on vacation like Transcription Factor is.

Thursday, April 5, 2007

The Central Dogma

The Central Dogma of Biology was first proposed by Francis Crick in 1958. It deals with the flow of information in biology. Since this is supposed to be an introduction, I will not go into the nitty gritty of the central dogma, noted exceptions and such. Let's look at the different steps in my depiction of the Central Dogma.

DNA is a (bio)chemical way of storing genetic (biological) information. It is basically a long stretched-out molecule consisting of modules (nucleotides, or as they're often called: bases). There are only four modules in a DNA molecule and they are the language in which the information is stored. The four nucleotides of which the DNA strand is composed are Adenine, Cytosine, Guanine and Thymine. The DNA molecule really consists of two strands of this long molecule, twisted into a helical shape. If on the one strand there is and Adenine (A) at a particular position, the other strand always has a Thymine (T) at that very same position, across from the A. The A and the T are chemically bonded to each other by 2 hydrogen bonds. In the same way Cytosine (C) and Guanine (G) always pair up using 3 hydrogen bonds. Because A always bonds with T, and C always with G, one only needs to know the sequence of the nucleotides on the one strand to know exactly what the sequence of nucleotides on the other strand will be. What I will refer to as a gene later on, is simply a stretch of DNA, with a start and an end.

The pretty picture of the DNA helix above is credited to brian0918 and was taken from

As cells divide, they need a duplicate of their genetic information, their DNA. To do this, the DNA helix is separated and a protein complex reads the information on the one strand, to produce the other strand (this is called the complementary strand). Since the same is done to both of the original strands, after DNA replication is complete, there are two copies of the original DNA molecule(s). After all the DNA in a cell is replicated, the cell can divide in two, which each half getting a complete set of DNA.

Transcription of DNA refers to production of a molecule called RNA, which is similar to DNA, but different in a few respects. Only one strand of RNA is made at the time, instead of 2 during DNA replication. RNA does not have any Thymine, but uses Uracil (U) instead. And lastly, each RNA nucleotide has a slightly different chemical make-up than a DNA nucleotide, it is made up of ribose sugars, instead of deoxyribose sugars like DNA.

Reverse transcription
Reverse transcription is the process by which an RNA molecule is read and converted into DNA. Retroviruses use this method to convert their genetic information, which is in the form of RNA into DNA. The DNA can then be inserted into the genome of the host. Handy tool, isn't it?

During the process called translation, a particular kind of RNA molecule (messenger RNA, mRNA) is read by a large protein complex called the ribosome. The ribosome "reads" the sequence of nucleotides, and stitches together strings of amino acids, one for every three nucleotides it has read. The amino acid strings are called peptides, or proteins and fold up into complex three-dimensional structures. These proteins are the big workers in the cells. They carry out all chemical reactions, including the processes described above of replication, transcription, and translation. Proteins are the workhorses of the cell.

Several steps back

Just before falling asleep last night I realized that I should take several steps back and explain some biology basics before jumping into my frustrations with microarrays. Although no one may ever read this, if some non-biology major comes along, I would like her/him to understand what I'm talking to about. In general I feel science needs to be more accessible to the general public, and I don't think I'm helping if I just start blabbering jargon.

So, I have decided that before continuing with my microarray story, I'm going to write several posts as a post-introduction to the topic.

Wednesday, April 4, 2007


A few years ago I gave up on a PhD in Molecular Biology and settled for an MS. Then I switched to a more applied field of study. It's going ok I guess, but MolBiol is still my first love. Last year my current PI collaborated with another lab to do a microarray study. He did not want me to have anything to do with it, because it would distract too much from my current project, and right he was. However, where do you find somebody who is comfortable with both expression data *and* our system?

My PI asked me if I knew anybody who could analyze the data. Hmmm. Well, I could really only think of one person in this neck of the woods and it would be... me. He was reluctant and said he would ask someone else for advise, but the second and third (and possibly fourth) person he asked referred him back to me. It took him a full 6 weeks, but unable to do it himself, he handed over the disks and asked me if I could take a look at the data. It was all I could do to not climb on the roof and let the world know that I'd be looking at the data. How cool is that! I didn't let on though and casually said that I would try and make some time to look at the data.

The first time I tried to open one of the files my 7-year old laptop crashed. Subsequent times weren't more successful, so I had to resort to something more capable of opening Excel files that were a little on the large side. Several days later I finally managed to lay claim to the lab computer (being a parent does not often allow me to go back to the lab late at night), and open a file. It took several minutes to even open. Scrolling down and to the right and back up and to the left. Numbers, lots of numbers. A few labels and more numbers. I closed the file and opened another one. Same result. I was kicked off the computer by the lab manager who had something to do. So much for my first glimpse at the data.

It took me a few days before I dared open the file again. Where to start? There are so many numbers! In retrospect I am the lucky one. Someone else got to do all the dirty work. The RNA isolation, reverse transcription into cDNA, labeling, hybridizing, all that good stuff. Better yet, someone else did the statistical analysis. All I have to do is interpret it. Should be easy right? But staring at hundreds of genes being differentially expressed is a bit overwhelming. Scratch that. *Very* overwhelming.

For several weeks I did not open the files again. I just mulled it over and over in my mind. Trying different ways of looking at the data, hoping something would jump out at me. There is no way my PI is going to pay for me to attend some kind of fancy conference to learn something about this. I'm on my own here. Re-inventing the wheel. I chopped the files up in smaller pieces so I can now manage them even on my ancient laptop. Then I started sorting and re-sorting the data. Just making different lists. To be continued....


I have three kids. For purposes of this blog, I'll call them F1-1, F1-2, F1-3. As I write this, F1-3 is busy wacking the mirror with the thermometer she found this morning. She's been busy measuring the temperature of all the bears and the dolls in the house, and I guess she figures that now that she knows everyone is healthy we can get rid of the measuring device. Since I'm too busy typing away, I just let her. In a few minutes I'll figure out if it's still intact. This could of course be an indication that she will turn into a good scientist. To measure is to know.

There's gotta be a first post

So, what to write? I've been wanting to start my own blog, my own corner of the blog-world for a while, but never really got around to it. Who wants to listen to my endless rants anyway? But this blog isn't for anyone else but me. My outlet, my corner. And so, here I am. If you're here too, welcome. If not, welcome anyway.

Some basics.
As I said this is my corner of the blog-world, and I rule. I strongly believe people have a right to speak their mind, but I am opposed to being hurtful. Therefore I reserve the right to delete any or all comments that I find hurtful or inappropriate.