Thursday, May 31, 2007

Thoughts on infidelity

I started typing out a comment to this post by Paul, but it turned out to be so long, that I figured it needed it's own post.

Paul wrote the following with regard to people who cheat on their partners:

"if you were so incomprehensibly foolish as to freely, and while sober, promise someone that you will remain faithful to them, then you should remain faithful to them. No excuses. You made the promise. Keep it.

That's Plan A.

In life, Plan A doesn't always work, and so most people always try to have a Plan B. Here, then, is Plan B: If you do cheat on your partner, then do so in the most ethical and responsible manner still possible."

In one of the comments, brandone stated:

"I think that anyone with the self-awareness and conscientiousness to successfully pull off Plan B also probably has the inner resources to hold fast to their promise from Plan A."

In principal I agree with brandone. But there is more to it for me than that. I also firmly believe it is the responsibility of the person making the promise to keep it. Therefore, if person A cheats on person B with person C, then person C cannot be blamed for this. Person C never made any promises to person B, but person A did. Does this make sense? It is fully person A's responsibility to keep his/her promise.

Having been around the block a few times, I know that if I feel a strong desire to cheat on my partner, there is something inherently wrong/lacking in my relationship and would consider that serious cause to break up.

Nothing is more important to me that the need to trust completely and be trusted completely. I would therefore also question the long-term viability of my relationship if I felt I had reason to be jealous (i.e. was worried about the possibility of my partner cheating).

I was in an extremely abusive and controlling relationship for several years, and both my son F1-1 and I am still paying a very high price for that. I will no longer put up with jealousy from my partner, it is simply an indication of lack of trust. This "I'm only jealous because I love you so much, you should be worried if I don't care any more what you do" is utter nonsense. And how about "I trust you, just no one else?" Bullshit. Cheating takes two people, and if you can't trust anyone with me, you don't trust me.

Don't get me wrong. It's not that I don't find anyone else attractive, it's just that I choose not to act on it. In fact, I have found it is a great diffuser of any feelings of attraction to a "person C" to just tell my husband about it. "Hey sweetheart, you know, I think person C is very cute." Suddenly a level of mysteriousness and secrecy disappears and the attractiveness changes into something funny, and my husband and I can joke about it.

In short. If you promise not to cheat, don't. If you can't keep your promise, you shouldn't be making any promises. And then maybe you simply don't belong in the relationship you have.

Arrays and more arrays

Don't get me wrong. I absolutely love going through sequences and trying to find patterns. And like Sandra Porter, I love analyzing sequences. But I have been working for months on thousands of sequences, and right this moment it is getting a bit much. Taking this break should help. I promised my adviser I would get the next step of my analysis back to him late last week, and I'm still working on it. It didn't help that one of my files got corrupted while I was saving it to my departmental server, and I lost hours and hours of work. Messing up an enormous spreadsheet was probably not a good idea either, I've spent an entire day cleaning up that mess.

I don't have any software available to analyze this data quickly for me. Someone else in my department told me I could try and use the program for which he is getting a one-year license. But he wasn't sure himself what the software would do, and therefore couldn't tell me whether it'd be useful.

So, I'm doing it by hand. Data from 8 slides with each about 44,000 genes on it. Granted, not all of them are differentially expressed, in fact not even close to all of them. But still, it's a respectable amount of work.

Well, at the very least it's pushed dementors far from my mind today. I'm guessing I have at least a couple more hours of work to do on this phase. And then I should be able to submit to my adviser a list of genes that we might consider looking at in more detail. He wants to submit a research proposal based in this information by July, so I'd better get back to work now.

If I've bored you, sorry, but this blog is more for me than for anyone else.

P.S. If anyone knows of any amazing, relatively inexpensive software to make my analysis of microarray data easier, this would be a great time to leave a comment here. Basically, the statistics has been done, I just need to make sense of the data, and maybe display the lot in a visually appealing way.

Wednesday, May 30, 2007

I need chocolate

Do you know what it feels like to be around a dementor? I do. I had opportunity this morning to be in the vicinity of my abusive ex-husband and that is exactly what it must feel like to be near a dementor. I'm still feeling somewhat jittery. I guess I should go to the fridge in search of a big chunk of chocolate.

UPDATE: Luckily Knobody came to the rescue, chocolate was provided for (with coffee too!), and I feel much better now.

Friday, May 25, 2007

Not a baby anymore

Today is both a happy and a sad day. The happy part: F1-3 turned 2!! The sad part is, I don't have a baby anymore. She's so grown up. She had a great birthday. I've been practicing with her, so she can say "2 years." She came pretty close, and at least she knew the general sounds to make when asked how old she will be.

I brought a Dora The Explorer cake and party hats in to her daycare in the afternoon, and we all sat down for birthday cake with our party hats on. We sang the birthday song, and got cake and butter creme all over our faces.

At home, we did the whole routine again with the leftover cake, the three kids, and P1. Then she unwrapped her gifts. She was very good at unwrapping, and her face lit up at the sight of the loot. Her brand new purse was a favorite, and was immediately slung over her shoulder. The bath toy and doll house were appreciated too.

Happy birthday my sweetheart. May you always be such a warm, caring human being and so full of joy.

Listen to your genes

To try and make science more interesting for the general public, researchers from the Department of Microbiology at the University of California have developed a program that converts DNA sequence into music. The results of their pilot project are presented here. More than just a curiosity, this may also help blind or otherwise impaired people interpret sequence data.

The group also links to their own website where you can translate your own gene of interest (goi) into music. The gene sequence needs to be in FASTA format, so it should look something like this:


Spaces are allowed, letters can be in uppercase or lowercase, a maximum of 4000 letters can be processed. The file will open right away and play for you, and it will be sent to the e-mail address you provide. Very cute. I just tried my own favorite goi, and it sounds great. I can't seem to figure out a way to post my music here. HT to VWXYNot?

UPDATE: Found a way to put the music to my goi online. Ha! Google has free webpages. I created one for myself, so I can link to stuff there. So here it is.

Thursday, May 24, 2007

A new way to find a job

Bora found a new way to get a job in 3 easy steps.

1. Write a blog post stating you want the job, so the future employer can ask if the post should be considered a job offer in the comments.
2. Write official letter of application.
3. Visit for interview.

Mission accomplished. Congratulations to Bora and PLoS! And he gets the best of two worlds, he gets a San Francisco salary, without San Francisco cost-of-living. He'll have to post a picture of himself in his pajamas before it can be determined whether they can be deducted as work-related expenses.

Wednesday, May 23, 2007


Yesterday I was peering through the weeds in my garden and look what I found:

Zucchini #1 (the smaller one of the two) weighed 3.5 lbs, while zucchini #2 was 4.1 lbs. Not bad for my first serious shot at gardening around here. I never noticed the two monsters until yesterday. Maybe I let them grow a little too much. That's enough zucchini to feed the family veggies for several weeks, and there are more where those came from!

My dear husband had some cute remarks about them that are probably not fit for a blog, but feel free to use your imagination.

Friday, May 18, 2007

Special Links for Special Parents taking care of Special Kids

I'm planning to accumulate a set of links specifically for parents of children with special needs. They will not be comprehensive, but rather skewed towards the special needs of F1-2. To begin with, a website with slideshows that children can go through by pressing the spacebar, clicking the mouse or touching the touchscreen. Last December my parents got F1-2 his own touchscreen here. He has shown limited interest in the screen, but that may be because we had little of interest to him on the computer. I had made up some slideshows for him myself with different shapes and colors, but he seemed more interested in pushing the buttons on the monitor to adjust monitor settings than the fancy touchscreen. On advice from his speech therapist, we recently got F1-2 software called Kidspiration. I'm meeting with the therapist next week to see how we can use it to improve his communication skills. More links will be added as I come across them.

Sudden Oak Death

Thanks to The Voltage Gate, the host of Oekologie #5, here is a link to a video that explains the status of Sudden Oak Death (SOD) in California.

SOD is a devastating disease of oak, caused by Phytophthora ramorum, a member of the Oomycota, briefly described in a previous post. Initially reported in Central California in 1995, P. ramorum has been found in Oregon, Washington, New Mexico, Texas, Colorado, Arkansas, Alabama, Louisiana, and as far East as Tennesee, Virginia, North Carolina, South Carolina, Virginia, Florida, and Georgia [SPDN]. P. ramorum has a wide host range (the disease can infect many different plant species). Some other hosts of the pathogen may not show symptoms, which makes it easier for the disease to spread.

[Image Source]
In some areas of California, 90% of the Oak trees are affected, and once symptoms appear, the tree often dies within a year a two. Phosphonates (or phosphites) are chemical compounds that can be used to treat plants infected with members of the Oomycota, and seem to be fairly effective against SOD. The treatment of full-grown trees, however, is difficult and expensive, so it is not very practical to treat large numbers of trees.

The spores of the pathogen are spread in wood, or by rain splash.

List of useful websites:
California Department of Food & Agriculture SOD Quarantine information
California Oak Mortality Task Force
The Southern Diagnostic Plant Network SOD webpage
USDA-Forest Service Pest Alert
American Phytopathological Society News & Views

Sunday, May 13, 2007

Happy Mother's Day

My parents started a family when they were very young. My mother dropped out of college and had a couple of kids, while my father was working on his degree. My mother stayed home with us until we were both in school. She attended evening classes to become a teacher. She had a number of jobs; her jobs working for an insurance company and as a high school teacher I can still remember (I was in middle/high school myself at the time).

After I had been in college for a couple of years, my mother decided to go back to school. She had started a degree in economics in the mid-late 60s, and now she choose to go back to school and get a BA in Public Administration. She had to take remedial math classes, and I tutored her. It can't have been a terrible teacher, because she scored easy A's for all her math courses. She finished her degree in record time, with flying colors.

Through it all, she managed to make sure both her kids attended track-and-field, swimming, tennis, ballet, gymnastics, and music sessions (I'm probably forgetting some). She would often spend virtually all afternoon driving us from one place to the next. Not to mention a couple of huge birthday parties every year. And home-made chicken soup or mashed potatoes with vegetables when we were sick. I took her dedication for granted at the time, but it really hit home when my brother got ill.

My mother and brother left the country, so that he could get better treatment. For almost a year, my mother spent every waking minute of her existence making sure my brother's needs were met, physically and emotionally. Nothing was too much for her if it made his day better.

I am now a mother of 3 kids myself, and I cannot begin to imagine what parents go through when they lose a child. I was there when my parents went this, but I was too busy grieving for my brother to notice. The next year of my life is sort of a blur, but I have a vague sensation of huddling close to my parents and a sense of shared grief, and trying to hold on to the memories of his life. What I do know is that one never gets over such a loss, one simply learns to live with it. And eventually one finds ways to be happy again.

My mother is getting ready to retire from her job at a bank soon. She is very active in the community, fighting against gender-inequality, and creating opportunities for women to further themselves, to become stronger, more self-sufficient. This is how she helps many other mothers.

She also has a lot of fun. She is singing, dancing, exercising, and doing all the things she never could when she had demanding, snot-nosed, ungrateful little kids running around. I rarely get to tell her this, but I hope that when I'm her age, I get to live as full, happy, and active a life as she is now.

When we were little, my brother and I would let my mother sleep in on Mother's Day. We would then serve her breakfast in bed, and bring her the presents we had gotten with help from our father a few days earlier. I remember vividly the scrambled eggs, the toast, the coffee. And I would take my guitar and play in my parent's bedroom what I'd learned the previous week. Now we live far apart, and I can no longer serve her breakfast or bring her presents on Mother's Day. But I can write this, and give her a call later. So ma:

Happy Mother's Day. Here's a rose for you:

Tuesday, May 8, 2007

DNA replication

This is how DNA replication should be explained (by David Ng)! Much better than anything I can put together. HT to coturnix.

Zen mom

Can someone let my beloved husband know that I'm considered Zen mom according to the latest quiz results:

Your quiz score makes you: Zen Mom How do you do it? Even when explosions are all around, you are able to take a deep cleansing breath and chant your mantra "this too shall pass." You are a calming influence on your kids in a hectic world.

Remember: Chatterbean quizzes are non-scientific, non-fat and pretty much just non-sense. They are meant solely for entertainment purposes and are not intended to provide an accurate evaluation of anything.

Spring semester over!

Well, Spring semester is finally over! All grades have been turned in, and presumably this means I will have my husband back. That would be nice. At least for a week, we can hang out. And then it starts all over again. Although, hopefully, it will never get as crazy again as it has been this Spring.

Friday, May 4, 2007

Oomycota are not fungi

Among the Oomycota (pronounced oh-oh-mycota), or oomycetes, are a number of very destructive plant pathogens, that have traditionally been studied by mycologists and were classified with the fungi, as "lower fungi."

The most notorious member of this group is Phytophthora infestans, the causal agent of late blight of potatoes, which was responsible for about 1 million deaths in the Irish Potato famine in the 1840s, and continues to cause losses in potato crops. Other examples are Plasmopara spp., and Peronospora spp. which cause downy mildew diseases, and Pythium spp., responsible for damping-off and a number of root rots on different crops.

These organisms were grouped with fungi for a long time, because they have a life style similar to that of the true fungi, getting their nutrients through absorption from their host or substrate. They also produce mycelium (the stringy, fluffy stuff often associated with fungi), which looks a lot like that of fungi, and they produce spores that look superficially like those of fungi. Sporangia are asexual spores from Oomycota and are formed on sporangiophores (see picture below). Under cool, wet conditions, short-lived zoospores with two different flagella can form within the sporangia. In the case of Phytophthora infestans, 20-50 zoospores can form within one sporangium, spreading the disease much faster than under warm, dry conditions, when each sporangium can only result in one infection.

Coenocytic sporangiophores with (asexual) sporangia from Peronospora sp.

Despite the similarities listed above, there are numerous differences between the Oomycota and the true fungi, and only fairly recently has DNA sequencing confirmed that Oomycota are close relatives of algae.

1. Oomycota are diploid (have 2 copies of each chromosome in one nucleus per cell), while fungi are haploid (have one copy of each chromosome in one nucleus per cell) or dikaryotic (two nuclei per cell, each with a haploid set of chromosomes).

2. The cell wall of Oomycota consists of beta glucans and cellulose, while fungal cell walls are predominantly made of chitin.

3. The mitochondria (organelles in cells responsible for energy production) of Oomycota have tubular cristae (internal compartments of mictochondria), while those of fungi are flattened.

4. Oomycota have distinctive sexual reproduction with oospores (that is where the name "Oomycota is derived from) that are fertilized by antheridia, while fungi don't have oospores, instead their sexual reproduction involves zygospores, ascospores, or basidiospores.

5. Zoospores (a different kind of spore also produced by Oomycota) have flagella that are distinct from those produced by true fungi if they do produce flagella.

6. Oomycota usually do not have cell walls between adjacent cells (they are coenocytic, see picture).

Fairly recent molecular evidence supports microscopic observations that indicate Oomycota are closely related to algae. However, mycologists continue to study these organisms in addition to the true fungi, mainly because their life styles are so similar. For plant pathologists, the newly revealed phylogenetic information has implications for population studies and control measures.

Rossmann, A.Y., and Palm, M.E. 2006. Why are Phytophthora and other Oomycota not true Fungi?
Feature Story May 2007 on APSnet
Kendrick, B. 2000. The Fifth Kingdom. Mycologue Publications. Online version.

Shaken baby syndrome

I noticed yesterday that someone found their way to my blog by searching for the term" meaning of shaken kids," strangely enough because of my post about my son learning to shake his head to communicate "no." I then did a quick search on Wikipedia on the shaking of kids. Just reading it, made my stomach turn, and I could almost not finish it.

So whoever did this search, if you read this post. Here are the facts:
1. Kids are very fragile human beings.
2. They have small, developing brains.
3. Shaking kids can cause bleeding of the brain
4. Even a small bleed can cause severe brain damage, including blindness, cerebral palsy, motor skill defects, and death.
5. I know what life is like with a child with disabilities, and I know what life is like for my child.

Whoever feels the need to shake a child. STOP! Take a break, go for a walk, call a friend, splash water on your face, step on your toes, do whatever it takes to take your mind off of this, and don't shake the child. More shivers up my spine.

Broken record

That's what I'm starting to sound like: vaccinate your children. Three cases of measles have been reported in Alachua County, Florida, all of which in people who were not immunized. One of the cases concerns a student at the University of Florida, who has been in contact with the Hare Krishna's providing food to students at the busy Plaza of the America's on campus. The Hare Krishna's have been asked to suspend their services for a few days to ensure no further spreading of the disease is possible. One of the other cases concerns a student of Santa Fe Community College, also in Alachua County.

The only way this outbreak was possible, is because people were not immunized, and if you live in that area, you're only at risk if you're not immunized. On the one hand, I don't want people to start panicking unnecessarily, on the other hand, I hope this has some impact on those who are trying to convince parents not to immunize their kids.

Update May 8: There are now 4 confirmed cases.

Superstitious nonsense results in death

In the small country of Guyana on the Northern coast of South America, a 55-year old woman, Radika Singh, was beaten to death by inhabitants of the village of Bare Root. A couple of reports on this incident can be found here and here. She was believed to be an "Ol Higue," a vampire-like evil spirit, there were reports that she had bitten a baby. The family of the woman told reporters that she was a quiet woman who never bothered anyone, but had a mental breakdown a few years ago. The woman was encircled by villagers, beaten with a broom, and left to die by the road side. Apparently, she was then sprinkled with some kind of flammable material and set on fire, the grass around her body showed burn marks when she was found.

I find it hard to believe that people believe in this nonsense. But most disturbing is the cruel reaction of the villagers, and that nobody thought it necessary to step in and help this woman. A clear example how mass superstition kills people. There were, not remarkably under these tragic circumstances, reports that the woman did not retain a human form upon being burned, and that she turned into a hair ball, before turning back into human form. And to dispute the allegations that the woman was a vampire, her family insists that this is quite impossible because she was a properly baptized christian. Go figure.

It leaves me utterly speechless.

Wednesday, May 2, 2007

String Theory

I never did get this String Theory thing. Until today. Discover Magazine has a contest for explaining String Theory in two minutes or less. You can see the six finalists here. Personally, I like "Vibrating strands of energy" and "The problem with math." It has also piqued my interest in the Large Hadron Collider.

A communist book

One morning I took my son to his therapy session, and was sitting in the waiting room until he was done. One of the parents there was telling another parent a story.
Her son goes to public school, and her husband wants to take him out of school and home school him. The reason?

Well, one of the books of the week was called "The rainbow fish." We have some version of it too.

It's a story about a fish with shiny scales, who doesn't have any friends. Once he starts sharing his shiny scales with the other fish around him, they all become friends. Now every fish has one shiny scale, and they play happily ever after. The husband of this woman objected to the reading of this book in his son's class because it's communist. The teachers are trying to make a communist out of his son. Why should anyone want to share anything? They're his scales after all!

The Rainbow Fish by Marcus Pfister (obviously a communist)
ISBN 0-7358-1299-3

Tuesday, May 1, 2007

Carnival of the Godless #65

While I go and do some research, you can go ahead and check out the newest Carnival of the Godless (#65). That should keep you busy for a while.

मकिता (makita)