Blog break

Since I'm currently located in a country in a warm climate, with lots of good entertainment, food and alcohol, and sadly, less than perfect internet connections, I am forced to take a break from blogging. I should return the first week of January, provided I sober up enough to post something remotely legible. Have a great start of 2008!

Plant Pathology: Gene-for-gene theory

Here is finally the post I promised that I had wanted to write for quite a while, and can finally write because it was one of the questions on my PhD qualifying exams.

In the 1940s, Harold H. Flor, made a large number of crosses of flax rust races (this is not a trivial exercise, you try mating these minute fungi with each other). He then identified how pathogenicity (the ability to cause disease) on flax was inherited (1). He would use all the flax rust progeny he obtained to infect (inoculate) a large number of available flax lines, and he would score the reaction of the plant to the pathogen (immune, resistance, semi-resistant, susceptible).

If that wasn't enough, Flor also made a large number of crosses of the host, each of which was resistant to none, one, or several races of the flax rust pathogen Melampsori lini. So, he would cross two races of flax, cross the resulting progeny with itself, and analyze the second generation. The reason for this is that the genes involved are often dominant and that you do not see the effect of individual alleles in the first generation (if that doesn't make sense, leave me a note in the comments, I'd be happy to elaborate). In the second generation, the recessive genes segregate and you can see all sorts of fun stuff going on. Flor inoculated all the second generation flax progeny to study the inheritance of resistance. He published those results in a separate paper (2).

Flor found that both resistance in plants as well as avirulence (= lack of virulence/pathogenicity; does not cause disease) in the pathogens were inherited. He also noted that even if the plant had a resistance gene (R), it was only resistant if the pathogen infecting the plant had a particular gene, which is now called an avirulence (Avr) gene. That's kind of weird, isn't it? If the plant has a resistance gene, why should it not be resistant to the pathogen all the time?? Flor also found that in almost all the cases he looked at, resistance was dominant over susceptible, and avirulent was dominant over virulent. Note: Flor used the word "factor" instead of "genes."

Based on Flor's results he formulated what is now called the gene-for-gene hypothesis (3):
For every gene in the plant that confers resistance, there is a corresponding gene in the pathogen that confers avirulence.

Since the genetics of both the host and the pathogen need to be taken into account, we pathologists put this in a quadratic check like this:










On the top row are the possible genotypes of the host. Flax is a diploid organism, i.e. it has two copies of every chromosome. As a result, there are two alleles of every gene (one from each chromosome), so the host can be RR (homozygous resistant), rr (homozygous lacking resistance), or Rr (heterozygous, one allele confers resistance, the other does not). Because resistance is dominant, the Rr plant will be resistant and react no different than the RR plants. The same argument goes for the genotype of the pathogen which is given in the first column of the quadratic check, with AA (homozygous avirulent), aa (homozygous virulent), and Aa (heterozygous, one allele confers avirulence, the other does not; the pathogen will act completely avirulent, because A is dominant over a) possibilities. The only way the plant is resistant is if it carries an R gene, and is infected with a pathogen that carries an Avr gene. In all other combinations, the plant will get disease.

From an evolutionary point of view this makes little sense. Microbes propagate very rapidly compared to the host. Why would a pathogen hang on to a gene that will prevent it from making a set of host plants sick? Why why why?? Microbes evolve so fast, you would think that pathogens with mutations of the Avr gene would have a distinct advantage over those that have a functional Avr gene.

The answer to this question is that Avr genes serve some other purpose in the pathogen, or are actually genes that contribute to pathogenicity, except of course, when it is recognized by the host. The exact same gene can therefore be a pathogenicity in one host-pathogen interaction, and an avirulence gene in another. An example of this is Avr4, an avirulence protein from the plant-pathogenic fungus Cladosporium fulvum. The pathogen is avirulent (cannot cause disease) if it has the Avr4 gene, and if the host it is trying to infect (in this case tomato) has the Cf-4 resistance gene. A recent paper (4) showed that if the Avr4 gene is deleted, the pathogen becomes less virulent, and that introduction of this gene in plants, made the plant more susceptible to a number of other pathogens. Avr4 therefore only contributes to resistance if the host has the corresponding resistance gene, Cf-4, otherwise Avr4 is a virulence factor.

The evolution of R and Avr genes is the result of an arms race going on between host and pathogen, where the host tries to prevent the infection, while the pathogen tries to bypass the host defenses to make the host sick (5,6). This can result in evolution at a pace higher than you would expect without this constant battle.

More on avirulence genes in my next mega-post. Which shouldn't take too long to appear, I have a rough skeleton already. In yet another post I will give some examples from Flor's original papers, and explain how he deduced the genetics of the host and the pathogen. The number of crosses he did is mind-boggling.

References:
(1) Flor, H.H. (1946) Genetics of pathogenicity in Melampsora lini. Journal of Agricultural Research 73: 335-357.
(2) Flor, H.H. (1947) Inheritance of reaction to rust in flax. Journal of Agricultural Research 74:241-262.
(3) Flor, H.H. (1955) Host-parasite interaction in flax rust - its genetics and other implications. Phytopathology 45:680-685.
(4) van Esse, H. P., Bolton, M.D., Stergiopoulos, I., de Wit, P.J.G.M, and Thomma, B.P.H.J. (2007) The chitin-binding Cladosporium fulvum effector protein Avr4 is a virulence factor. Molecular Plant-Microbe Interactions 20:1092-1101.
(5) Maor, R, and Shirasu, K. (2005) The arms race continues: battle strategies between plants and fungal pathogens. Current Opinion in Microbiology 8:399-404.
(6) van der Does, H.C. and Rep, M. (2007) Virulence genes and the evolution of host specificity in plant-pathogenic fungi. Molecular Plant-Microbe Interactions 20:1175-1182.

My gift

Last week I got my gift from Sciencewoman in the mail. Thank you Sciencewoman. I really enjoy reading blog, you're a true superhero. And then to get a gift, is a nice bonus.

To add to the excitement, the gift has an interesting story too, which I would like to share.


The bookmark was made out of recycled junk mail, with a cancelled stamp from Benin, by another female science blogger (woohoo!). She also has her own online crafts store: Recycled Ideas, where everything is made out of recycled material. This is a great way to find gifts to show you're giving in an environmentally friendly way.

Thank you Sciencewoman, what a great and thoughtful gift. Now if only could find time to read a book to use the bookmark with. I suppose for now, it'll have to be put to work in scientific papers.

Holy Pasta and Authentic Sauce

The American Academy of Religion held it's annual meeting in November. And some students from the Universities of Florida and Syracuse presented their research on the church of the Flying Spaghetti Monster.


It is about time that the church of the Flying Spaghetti Monster is taken more seriously. How else are we supposed to learn about the effect His Noodly Appendages have on our daily lives?

Cephalopod tricks

I need to learn this skin-changing trick. Imagine all the naughty things I could do.

Two down

I finally turned in my second exam. It was a strange one. The professor did not give me a deadline to complete the open-book exam, so I had to write, until I thought it was enough. But when is enough, well... enough? With six questions, rather broad in scope, there seemed to be no end to my writing. I could have written a book on each of the questions. Eventually I just gave up, and turned in what I had. Hopefully it will be adequate. I suppose I prefer a deadline. At least then I can do the best I can in the time available, and no more. The exam also had a closed-book section, so I did that on Friday. Tomorrow morning the next exam should come in. I can hardly wait... not.

UPDATE:
F1-3 woke up this morning with a high fever and nausea. So much for working on exams today. I don't remember her ever being this cranky. She has been inconsolable for hours now, and complains that her eyes hurt. I scheduled a doctor's appointment for this afternoon. In the meantime, I serve no other purpose in life that being the hanger she has suspended herself from.

UPDATE 2:
F1-3 cried for almost 3 hours straight, at which point I scheduled an appointment and took her in to see the doctor. Strep throat, accompanying rash. Antibiotics. Contagious for another 24 hours after starting meds. And to top it all off, when we changed F1-2, we noticed the same rash, and he had a slight fever. It looks like I'm home at least through Wednesday with 2 sick kids. This should make for an interesting qualifying exam.

UPDATE 3:
F1-2 definitely has Scarlet fever. Just lovely. And this morning he had 4 seizures. I spent the entire morning at the doctor's office with him. My exam came in Monday night. I have a week to answer 1 question. And it's not exactly an easy question either. I haven't even had time to do a basic literature search yet. Ready, set....go!

Get a new brain

Cuttlefish is showing us a new way to get a substitute for those of us who could use a replacement. Brilliant!!

And I copy-and-paste (but you should go and check the picture at cuttle's blog):


We’ve got sweaters to mend; we’ve got socks we can darn,
So pull up a chair, and I’ll spin you a yarn;
It’s a song with a Scarecrow-of-Oz-like refrain:
Please pick up your needles and knit me a brain!

I’ve knitted my bones, and I’ve knitted my brow,
But I’ve never seen brains knitted—up until now;
With each neural pathway a separate skein,
It’s Art and it’s Science, so knit me a brain!

Two hemispheres knit, and then reaching across ‘em
A beautiful, zippered-up corpus callosum;
Such fine application of knit, purl, and chain,
I want one myself—so please, knit me a brain!

With the brain’s convolutions appropriately gyred
This fabric creation has got me inspired!
My love for this art, I can hardly contain—
So how can I get one? Please knit me a brain!

Some people may tell you I’ve gone ‘round the bend
That the stuff ‘twixt my ears needs some decades to mend.
I could use some new grey-matter; mine’s gone insane,
It would not go to waste, if you’d knit me a brain.

You can see for yourself—why, just look at the time
I must take to obsessively put things to rhyme;
Something’s wrong, and I think that the answer is plain:
I need a replacement—so knit me a brain!

Fall photoshoot

I'm posting a link to the picture of my daughter, F1-3, taken in October at daycare. However reluctant I may be to post pictures of my children, it felt unfair to withhold this from everyone. Click on the link below. It will not work at first. Remove *every* occurrence of the word "lock" in the web address to get to the actual picture. The word occurs twice in the address. I will keep the photo up for a week or two, then remove it.

Introducing..... F1-3

Unexpected benefits

Those of you lamenting the scarcity of science-related posts, rejoice! I just received my second qualifying exam today, and although that may sound like terrible news, one of the questions is actually a post that I have been wanting to write for a long time. So, I think I will simply post my response to the exam as a science-related post. How cool is that? The bad news is that I first have to finish off some of the other questions, because I'm worried that I'll run out of time if I start on the fun ones first. So, hang in there, science coming up!!

The Truth

So, the writers at The Science Creative Quarterly offer us the the truth. I can't say I agree 100% though. In my experience, gin is better than whiskey. Other than that, I'm all with them.

One down

Well, for better of worse, I just submitted my first written qualifying exam. It's not my most brilliant piece of science writing ever, but it's not the worst either, so I think I'll pass. Some of the questions I answered in a lot more detail, because I already knew quite a bit about it, so it was much easier to come up with relevant publications, others were totally out of my league, and I just fumbled through. Now I'm going to take my first shower for the day (it's almost 6 pm!) and then I'm going to spend what's left of the weekend with my kids. I've shoo-ed them away too many times today. On Monday, I get the next exam.

The real price of quals

After my first pregnancy, I was back to my original ~115 lbs weight within about 3 months. After my second child, it took me 6 months to get back to my pre-pregnancy weight of ~118 lbs. Now, finally, almost 2 1/2 years after the birth of #3, have I made it back to my pre-pregnancy weight of 124 lbs (down from 166 lbs on the day of her birth). Ignore the gradual increase in weight as time progresses, I can live with that. Just focus on the 124 lbs.

Since I started writing my qualifying exams, I have done nothing but eat, snack, eat, snack and drink while I write. It doesn't help that we have loads of Halloween candy left, and I can't stop. I'm facing a month of qualifying exams. Would anyone hazard to guess what I will weigh on December 13th when this is all over? Or how much I will weigh after the winter break? Feel free to leave estimates behind. I promise I will weigh myself on December 13th, and put up an honest answer (shudder...)

Dang, didn't work again

You see, prayer really isn't all that effective. Of course, this can be explained by the fact that the 250 people praying weren't *true* christians. They just didn't believe strongly enough. Or one of them was gay, which--needless to say-- is such a terrible sin that Georgia needs to go without rain for a while longer. Or.... you could go on and on, but when rain does come (let's say in a month or so), you can bet your ass that they will claim that their prayers are to be credited for this miracle. Sigh... back to writing qualifying exams about real science. Maybe it'll offset some of the ignorance and stupidity out there.

The joys of trying to obtain a PhD.....

...my written qualifying exams start tomorrow. And will continue to at least December 13th. Will somebody please remind me why I decided to put myself through this again? Sadly, this likely means that blogging will slow down (more), except for frustrated rants about quals. And the fun does not stop there. Oral qualifying exams are scheduled for February 14th. Can someone remind me...?

Is this ethical?

Ok, this is the post where I hope all lurkers will come out and give their opinion.

Someone I worked with in the past has asked me to help write a couple of scientific papers, and has offered to pay me for it. This person is not a very good writer and apparently thinks I am (I'll take that compliment anytime). The individual in question would send me the results of the research (draft figures and tables), and I would do the writing (i.e. literature review, results, discussion, and conclusion). It is a field that I worked in for a number of years, so I'm fairly familiar with the background.

I cannot accept pay for two reasons:
1. I cannot legally work in any other capacity than as a graduate student.
2. This individual is a good friend, who has helped me out tremendously in the past, and it just wouldn't be right to accept money.

A colleague has suggested that in lieu of pay, I ask to be a co-author on the papers. To the best of my knowledge, it is not normally done to include people as authors, unless they have actually done some of the experiments (the main exception to this often being the principal investigator, who presumably is the main brain behind it all).

What do you think I should do? Should I ask to be a co-author, or just do this (it is a lot of work!) out of the goodness of my heart? Or should I not get involved at all. Comment away. Let it be known that my husband thinks the last option is the best. In his opinion I'm way too busy working on my own degree, and trying to take care of my family to be spending time writing someone else's papers.

Why I don't donate blood

Back home (more years ago than I care to remember) I used to donate blood regularly. As soon as I could, I was back on the bed with a needle in my arm donating every last drop of blood I had. When I moved here, it took a little bit of time to settle in, and eventually I donated fairly regularly again.

When my brother was ill, I desperately wanted to donate my bone marrow so that he could have a transplant and live. Sadly, no one in the family was a match, and eventually the only option he had was to receive his own marrow back. This, however, was likely no good, and he only lived a few more months after that.

When I learned that the US had an extensive bone marrow donation program, I called the local blood center to state that I would voluntarily have a hole drilled in my pelvic bone, so that someone could finally benefit from my bone marrow. To my surprise I was immediately rebuffed. Did I have the money to do this? they asked.

Huh? Money? What are you talking about? Well, to find out if I'm a match for anybody on the registry now or in the future, a number of blood tests needed to be done. Since there is no funding for these tests, I needed to pay for these tests, so the information could go into the database. How much are we talking about? $600. You've got to be kidding me $600, and I need to pay that in addition to lying in a hospital so someone can drill holes in me and harvest my marrow?

This is how it works, unless you have a particular individual in mind that you want to donate for. If preliminary tests show you might be a donor, then their medical insurance would pay for the additional tests. Since I just wanted to volunteer out of the blue without having anyone in mind, there was no funding for the tests. Except if you belong to a certain ethnic background, in which case there was a special program to find donors of the same ethnic background. I said that I am of just about any ethnic background you could think off, but that wasn't enough. End of story. I'm a poor graduate student (currently $3.22 in my checking account, and payday is two days away), and there is simply no way that I could conceivably come up with that kind of money if I wanted to. More than anything, it's the principle of the matter, and I think there is something horribly wrong with the system.

Fast forward a couple of years. I'm about to give birth to one of my children. I discover there are a couple of options for my infant's cord blood. 1. I could store it for some unknown medical purpose in the future that hasn't been discovered et, for which I needed to pay money to have it stored. Or 2. I could donate it, so that the stem cells in it could be harvested, and be put to good use. I choose option 2. But when the time came, it turned out that there was no way the hospital could store the cord blood, therefore it was unlikely to be of any use to anyone. Guess what? My child's valuable cord blood went straight into the garbage.

I protest. I no longer donate blood. I still am however an organ donor, in case someone decides to kill me in a car accident or something like that. Hopefully my organs will not end up in the trash can somewhere, but will be put to good use. And if and when I return home, I will gladly go donate blood again as often as possible.

Everything and more

Today I'm Superwoman. I do everything and more. This morning I got up early, and painted the south wall of my living room, I got three kids ready, and we left the house on time. F1-1 was dropped off at school on time, with his homework finished and checked, F1-3 was dropped off at daycare, received all the hugs she wanted, and I took F1-2 to therapy, we were actually 3 minutes early. Not a bad start of the day eh?

I already had a nice talk with my adviser this morning, which reminded me of how lucky I am to work for him. What a nice, decent human being. And not a bad researcher at that either.

I already did the PCR reactions I was supposed to do to sequence a tiny part of my favorite fungus' genome. I just got back from a lunch with someone who used to work in our building and has left for greener pastures. He helped me troubleshoot an electrical problem I'm having at home, and a problem I had connecting to my server share at the department. Now I'm off to the greenhouse to harvest the rest of my experiment.

All things considered not a bad day at all in terms of productivity. Not bad. I deserve a pat on the back [[reaches back and pats herself on the back]]. I wish everyone a great day!

F1-2 likes older women

Now that F1-2 is growing older, and his disabilities make him stand out more from his peers than before, it sometimes is just a little weird.

Yesterday we went to a restaurant with him for the first time in about 3 years (I think, it's hard to keep track, it may even be 4 years). And he kept on wanting to cuddle up with one of the older women at another table. I think older women remind him of his loving grandmothers, which is kind of cute.

However, it's not socially acceptable to go up to a total stranger to start playing with her earlobes. A sure sign of affection coming from F1-2, but try explaining that to the woman who just had her space invaded by a squealing kid, trying to pull out her earring! My husband had to go over several times to retrieve F1-2, but as soon as he let go of his hand, F1-2 would let out a loud, happy yelp, and limp back as fast as he could. He must have thought it was some kind of game. The woman smiled politely at him, and eventually he decided he had had enough. She wasn't as much fun as he thought she would be.

But wait, what about her?? And off he went to accost some other woman sitting nearby. Again, P1 had to go after him (I had my hands full with F1-3, so my husband was in charge of running after F1-2). This woman actually high-fived him. Oh well, so much for a nice family outing. To avoid further embarrassment, we packed up and left as quickly as we could. It will probably be another 3-4 years before we try that again.

Sibling rivalry

Saturday morning in our household. F1-3 says she doesn't want to eat her porridge. But the twinkle in her eyes tells me she's just teasing me, to see how far she can push me.

makita: F1-3, do you want another spoonful of porridge?
F1-3: Noooooo!!
makita: Are you sure?
F1-3: Noooooo!! (She means "yes" but "no" is one of her favorite words right now)
makita: Ok, never mind, mama is going to take it away if you don't want it.
(Mama starts to walk away with the bowl of porridge)
F1-3: No mama! Eden!! (Eden means "eat")

Two bites later she rejects the porridge again.
makita: F1-3, are you done?
F1-3: Yeah!!
makita: Ok, well I guess I'll just give it to F1-2 then. I'm sure he would love to have some more.
F1-3: Nooooo!!
And she proceeds to empty the entire bowl without further struggle.

1-0 for makita (thanks to sibling rivalry)

Complaints

If you cannot handle whining, this would be a great place to stop reading this post. I had my first PhD committee meeting in over a year, and I've never been more depressed or filled with self-doubt than right now.

Having already failed to finish one PhD program, I would have liked a little more smooth sailing this time. It seems that I simply cannot satisfy any or all of my committee members. My project has both applied and molecular aspects to it, hence I have faculty members from both ends of the spectrum on my committee. The "applied" faculty members think I'm doing way too much molecular work, while the "molecular" committee members think I'm not going into enough molecular depth.

It doesn't help that I had to move over to a slightly different course, because a huge part of the project was simply not working. At least one committee member is really upset about that change. It might have helped if he had been present at the last committee meeting, when I already mentioned the problems I was having with that part. I'm repeating the experiments as we speak, changing some of the strategies, but frankly I'm not optimistic, and it appears that this particular individual wants to me to approach it from several more angles before I move on.

In my point of view, however, my veering off isn't all that far-fetched, and I simply don't seem the points of going it over and over and over again, if I've pretty exhaustively shown the results are negative. In about 2 weeks I'll have the results of my latest efforts, and if they're still negative I would like to say I'm through with that.

It doesn't help matters that my committee is going to start sending over written qualifying exams in the next few weeks. Yuck! Did I say yuck? I meant yuck-a-dee-yuck-a-dee-yuck-yuck-yuck!!! Since I've already been through that torture once, I really am not looking forward to do it again, even if the field is different. I understand I have to, but that doesn't mean I have to be happy about it, and I'm not.

On the bright, there is one, there is always one - and I will bend over backwards to find the bright side of any situation I'm in- is that my professor is really supportive. He's been mad at me a few times, actually recently he was royally pissed at and disappointed in me, but in there he was behind me 100% Thanks boss, you have no idea how much that is appreciated. What a difference from my previous adviser!

He was telling me that one of the other members (who provides part of my funding, and therefore has to stay on the committee) is really pissed at him, and that he expected this person to take it out on me. Lovely, just lovely... But then again, if you don't get along with my adviser, there is something horribly wrong with you. He is one very cool dude. So, I say this other committee member is being unreasonable.

Ok, I feel better for having written this long complaint here. Back to the lab, back to the research. I have to write a 2-page project report and submit it by next week. I'll have to start on that tonight. Wish me luck, I need it. Now let's hope the kids stay healthy.

The source of the image in this post is The National Center for Atmospheric Research & the UCAR Office of Programs, and according to the statement on their website, I, the User, am "granted the right to use this Site for any non-profit, training, research, or educational purpose whatsoever -- and not for any direct or indirect commercial purpose or advantage -- without any fee or cost"

Blog Action Day: Environment

I grew up in a tropical third world country. Most of the country is covered in pristine rainforest. Sadly, ever increasing areas are being logged or destroyed by mining. It is sad. For a couple of years I left the capital and moved to the rainforest. It really brought the rainforest to life for me, in ways short visits never had before that time.

In the tropics plants and animals (especially insects) are a normal part of daily life, but the diversity in the rainforest is truly astonishing. On a field trip on day I saw the most amazing caterpillar. That is, I think it was a caterpillar, since it's main body was long and narrow. However, it was unlike any caterpillar I had ever seen before. It had huge colorful ornamentations, spikes sticking out from all over it's body. I must have stood there watching it for the longest time, not wanting to take my eyes off of it. Where is the damn camera when you need it anyway?

Another time a black panther (or jaguar) crossed the dirt road right in front of me. Amazing, the large glistening body, the muscles in his legs as he ran, the sparkle in his eyes. I'll never forget the sight.

Snakes are not uncommon in the capital, but in the rainforest you run across one virtually every day. Since I don't know how to distinguish most of them, I've always kept a polite distance from them. Crocodiles were frequently sunning themselves on the bank of the river where I lived.

And then one day I awoke to the sound of heavy machinery. Across the river trees were falling one by one, and a few weeks later the river bank was barren. It tore at my heartstrings. Isn't there anything anyone can do to stop this?

Many organizations worldwide condemn large scale logging in tropical rainforests. Understandable, but often demands are rather unreasonable. Logging and mining are responsible for a substantial part of the gross domestic product of nations that are struggling to keep their heads above water in the modern world. As developing countries we don't really want to cut down the entire forest, it simply helps to diversify our economies. Often poor countries perpetuate their poverty because their economies are not diversified enough to grow. Dependency on one or two major export products can be devastating if the market for one breaks down. Many people living in rich countries really have no idea what it is like to live as an underdog in an underdeveloped country. It is a constant struggly to prevent yourself from drowning in the maelstrom that is todays world economy.

This post is in memory of my father. He opposed the ban on imports of tropical hardwood from countries with tropical rainforests. He argued that if developed countries no longer import hardwood, it would greatly decrease the value of each tree. There would be no financial incentive for us to keep our rainforest as intact as possible.

The solution, in his opinion, is to encourage developing countries to maintain their rainforests by giving incentives for logging in a responsible manner (which is possible). Ideas he had were incentives for a minimum trunk size before logging, so that the trees had had plenty of opportunity to propagate. An adoption program, which would allow people to adopt trees, or sections of the rainforest in return for sustainable management. He argued that if hardwood has no value for us, we would ultimately have no choice but to cut down the rainforest to allow more lucrative ways to use the forest. The bottom line is, it is all a question of economics.

Responsible programs have been developed and are in use in tropical rainforests all over the world. Poor countries need financial incentives to implement these programs.

In loving memory of EAB (November 1944- June 2007)

5 gifts

I'm in. I'll send out a gift to the first five bloggers to comment here. It'll be interesting to see if I get actually 5. That'll be a record.

By the end of the calendar year, I will send a tangible, physical gift to each of the first five people to comment here. The catch? Each person must make the same offer on her/his blog.

From ScienceWoman.

Kind of catchy

Shorter shopping list

Big step this weekend! It looks like I may not be adding diapers to my shopping list quite as frequently anymore. Saturday morning 5 am, F1-3 woke up and was calling insistently for me, and she kept on saying "baddy." Not knowing what the heck she was talking about, I let her lead me to ...the bathroom. And indeed, after successful use of the bathroom, I put regular underwear on her, and she stayed dry virtually the entire weekend, with a couple of mishaps, more a timing problem than anything else. I did put diapers on her for her naps and at night, but I think the nap diapers are going to disappear soon, since they are often dry afterwards. She went in underwear to daycare today, I'm hoping the success will extend to daycare. Congratulations F1-3, great job!!

P.S. "Baddy" obviously means "potty." How could I not have picked up on that?

Not remarkable

My mother-in-law is in town for a week. This morning she came along while I brought F1-2 to school after his therapy session, so she could drop me of at work and use the car all day. She told me that she had seen some celebrity on tv who has a child with special needs (she told me the name, but I don't typically keep up with celebrity news, so it didn't mean anything to me). She told me how remarkable she thought this woman was for doing so much for her son. All the therapists she has, and all the wonderful things she and her son have accomplished as a result of that. Apparently many members of the audience commented on how much hope they derived from this woman's experience and how great it was bla bla bla.... My mother-in-law was ready to go on and on about this, when I interrupted her.

This does most certainly NOT fill me with hope. This very famous woman makes more money in a week than my dear hubby and I will make in our life. I look at my dear little F1-2 and see a sparkle in his eyes that tells me there is so much more in him than we give him credit for. But it requires a lot of time that we simply don't have, and probably will never have, because we have to work our butts off to keep a roof over our heads and food on the table. We will never be able to afford great therapists to work with him every waking moment to get every little ability out of him. And therefore, so much of what he is capable of will never come out. It is utterly depressing.

So many children out there with special needs do not have rich celebrity parents, and they are screwed. They will never reach their full potential. It does not fill me with hope that this woman could do it, although I'm glad for her son he does so well. I'm engulfed by sadness for all the thousands of children like my son who get left behind.

I think I may have have shocked my MIL. Obviously, she hadn't thought of it like that. But I do, and I feel guilty about not being able to spend more time with F1-2 to work with him, about not being able to afford more therapy for him, about the potential in him we will never witness. I'm so sorry my sweetheart.

Beat

Not the beat of tired (yet). My mother-in-law announced last week that she's coming to visit this Sunday. I had to finish off the guestroom/playroom in a hurry. As a result, the house is more of a mess than it's ever been before. With kids around it's impossible to clean up. They increase the mess faster than I can clean it up. So, this morning is dedicated to the house. And there is nothing to spur one on than the irresistible beat of Mark Anthony's album "Desde Un Principio." Ok, one needs to interrupt the cleaning activities with a few dance steps, but progress is far better than without the beat. Hey, and it's great exercise too. In an hour I'm taking a break to have lunch with my beloved. All things considered, it's a fabulous Friday in the makita-household. Just wanted to share my jubilation.

New Blogger

Everybody go and say hi to a brand new superhero on Scienceblogs: Sciencewoman.

Horizontal transfer

Horizontal transfer is very near and dear to my heart, since I worked on a bacterial self-mobilizing pathogenicity plasmid for years. This post by Conspiracy Factor on the uptake of DNA by higher organisms was an eye-opener to me. Exciting stuff.

Don't tase me bro!

Three days after the incident at the University of Florida in which a student was tasered by university police at the end of a Question & Answer session with John Kerry, the web is buzzing with claims that Andrew Meyer is an attention seeker, in the habit of taping his own practical jokes.

It doesn't really matter how much of an attention seeker Andrew Meyer may or may not be. It's irrelevant to what happened. Yes, he was making a nuisance of himself by asking questions when the Q&A session had been closed. But he was tasered after he had already been wrestled to the ground and was held by 5 police officers. He had at least one handcuff on already. At am minimum that is bad police work, at worst that is excessive use of force. Andrew Meyer did not pose a threat to anyone. The fact that he tried to pull his arms away from those trying to restrain him doesn't tell me anything. That would be a normal physical reaction to being restrained against your will.

The focus is being shifted away from the incident and towards Meyer's personality (flaws). Even though the Q&A session was closed, Kerry had already said he would answer the questions. It is unfortunate the opportunity to hear the response was lost.

God is facing the death penalty

This story on MSNBC and Wikinews:
Nebraska State senator Ernie Chambers sued god last week. " God inspired fear and caused “widespread death, destruction and terrorization of millions upon millions of the Earth’s inhabitants.” Senator Chambers seeks an injunction against god.

Senator Chambers filed the lawsuit in protest, because a judge forbade the use of the words "rape" and "victim" from a sexual assault trial. Whatever the reason, it's about time that god has to account for the death and destruction he has caused over the millenia. Attempts by Wired News reporter to contact God for comment were not successful.The only question of course is: which god did the reporter try to contact?

Ignorance in the library

I went to the public library today, to exchange some books on tape for other books on tape. For a change I wandered through the non-fiction isle. Now, this may not be my culture, so I may be wrong about this, but for some reason I always thought William Shakespeare's plays were fiction.

But the worst was yet to come. The shelf right above the one containing "Romeo and Juliet." There were titles such as: "God: the right way." This was not actually a title on the shelf, but one I've made up, however, you get the idea. There were numerous similar-sounding jesus and or god-praising title. Now what is this junk doing on the non-fiction shelf? I think I might write a complaint to the library. Something to the effect that I could not find my favorite god-fiction, because for some reason it was filed with "the other real stuff."

Speaking of feminism

This has been in the news lately:
http://www.cnn.com/video/#/video/us/2007/09/07/costello.mini.skirt.cnn
In short, a woman boarding a Southwest Airlines flight, was told her outfit was inappropriate. Uhh, so I looked at this outfit, not that it matters. It doesn't really matter what she was wearing for the purposes of this discussion. But I looked at the outfit anyway, and its not anywhere near inappropriate. Do they also ask men to change their outfits if their bellies are hanging over their belts? Or if their butt cracks are showing? This is so blatantly sexist, its unbelievable, and Southwest should be sued.

Moreover, why exactly does CNN's coverage add that she is a Hooters waitress. What does that have to do with anything. What sexist coverage! Southwest can consider itself boycotted by this blogger.

On another nerd's request

On the work front

Having lost more than a month this Summer to absence and general un-productivity, I've officially turned on the jet engines now. I'm busy isolating my favorite plant pathogen, and have a number of experiments lined up. I also have to call together my committee to explain my lack of results so far and to schedule my qualifying exams. Considering that I passed my qualifying exams in my previous program, I don't really feel like going through it again. But that's the nature of the game. On the bright side, since I'll be more engrossed in real science, more science-related posts are likely to follow. So now: back to the microscope.

Long weekend

Whereas other bloggers may have used the long weekend to catch up on some blogging, yours truly kicked into high gear and worked around the house. I got one side of a door painted, and both sides of another. I rearranged the playroom which had been used as sort of an storage area during construction. It is now fit to be a playroom again. The VCR meant for that room choose this weekend to die and go where dead VCR's go, so we got a VCR-DVD recorder combo to replace it. Yeah, why not go all out while we're at it. The kids, especially F1-2 is very pleased with renewed access to his favorite room in the house, with true entertainment at his disposal. I also, primed F1-3's room to cover up the paint, and layered two coats of bright yellow on top of it. After all, she is m sunshine :-)

During the painting process I did not bother to cover up the carpet. We were planning to rip it up in a few weeks anyway. But I had not expected to tip over the bucket of yellow paint on top of it. But that is exactly what I did yesterday. Oops! And there went the bucket, and the carpet. Oh well, time for drastic measures. I looked at the clock: 11 am. Plenty of time left in the day. I ripped up the carpet and the padding. I removed the tack strips, vacuumed the floor, got the concrete patch, patched the holes, and took a break for lunch. During lunch the concrete patch could dry, and after lunch I put down plastic sheeting to form the moisture block and started laying the laminate flooring we've had stocked up for a couple of months now. By 7 pm, I was done. Mostly, anyway. I still have a tiny little strip to do at on end of the room, but it takes a lot longer to cut the planks length-wise, and it was getting kinda late. Then I move F1-3's bed into the room, which up till then had been her big brother's.

So in less than a day I put on a layer of paint in her room and the flooring and swapped the kids from their bedrooms. Not bad, eh? I still have to put the finishing touches to her room, but it should be all done by tonight, or at the very latest tomorrow night.

Feminist

Big surprise here, right? HT to GrrlScientist

You Are 98% Feminist

You are a total feminist. This doesn't mean you're a man hater (in fact, you may be a man). You just think that men and women should be treated equally. It's a simple idea but somehow complicated for the world to put into action.

Are You a Feminist?

See what I mean?

Life around me really is never boring. Remember how happy we were that F1-2 was in a class with 4 students, 1 teacher, 2 aides, and 1 intern? It didn't last long. Yesterday I was informed that he class had been scrapped. Yes, scrapped. Now his class had 1 less teacher, and 3 extra students. The school board decided that the kids in his classroom were over-served, and decided to combine the two functional classrooms, ship his teacher off to another school. Now he is in a classroom with 7 kids, 1 (different) teacher, and 2 (different) aides. All of the kids in F1-2's room were non-verbal,they now constitute more than 50% of his new classroom, and the new teachers has very limited experience with non-verbal kids.

So why was the teacher better qualified to teach non-verbal kids moved to another school, one might ask. And the answer is, she had not been there long enough. Yep, the other teacher had seniority, did not want to leave, forget about having teachers to meet the needs of the majority of the pupils. We've got our priorities straight here. And we most certainly wouldn't want to involve any parents while these decisions are being made, they might point out these little anomalies that will mess up the way we work. And around here, seniority rules. We'll inform the parents once it's too late to change stuff. We can't swap the teachers anymore, F1-2's teacher has already been assigned to another school. Never mind that she is leaving kicking and screaming that she is concerned that the children's aren't being met.

So here we go, having to fight for our son's already shaky future. He is going to be in the same classroom for the most important of his formative years, from Kindergarten through 5th grade. Whatever we do now, will impact the rest of his life. Overly dramatic? Maybe. But it just infuriates me that decisions can be made based on anything except what makes the most sense for the kids. If it wasn't for the fact that his current school is the *only* school in the county with therapists on site, I would have demanded him going to another school.

We haven't made up our minds yet where to go from here, but you can rest assured that noise is about to be made.

Poop on the train?

When you're around me, life is never boring. There is always something going on. Boring is good, boring is good, boring is good.

About 3 weeks ago, I woke up from an afternoon nap, and noticed that the ring finger of my right hand was bent towards my palm, and I was utterly unable to straighten it. It was the weirdest thing. It didn't hurt, feel sore, or strange, I just couldn't bend it. Bizarre. I showed P1, and he insisted that should go to the campus health center right away. Yeah right, that's gonna happen. I already don't have absolute confidence in their abilities, and now I'm going to go with this minor problem? Nope! It''ll go away by itself.

Wrong. It didn't. In fact, every time I wake up it seems to have gotten a little worse. It gets a little better during the day. I can grasp the finger with my other hand and painlessly straighten it out, but as soon as I let go, the finger stubbornly snaps back down.

Yesterday I finally scheduled an appointment, and feeling self-conscious, and almost relieved that it had been quite bad when awoke today, I went to an early morning appointment. From the look on the face of the physician-assistant I've been seeing for years now, I could tell that she didn't believe a word I said. The twinkle in her eyes said "now there is someone with imagination who wants an excuse note for class or something." She must have been surprised to hear that I am no longer taking classes. She then said she wanted to have x-rays made (even though it doesn't hurt, and I did not injure myself). Whatever. I'll do what she says. I felt really, really stupid.

On our way to the x-ray room, we run into the physician in charge, and she says to me "let's see what he thinks." He looks at my hand for 2 seconds flat and asks me where I'm from. Huh? "What is your ancestry?" he asks when he sees the flabbergasted expression on my face. "Do you have an hour or so? I'm from all over the place." He says: "It's called Doo-poo-train's contraction, and its genetic. Most common in people of Mediterranean decent." Me: "It's called what?" He looks at me as if I'm an idiot, and then with proper pronunciation repeats: "Dupuytren's contracture." Ah, I must have misheard the first time when I thought it had something to do with people pooping on trains.

The PA and I walk on, so she can write a referral to a hand surgeon for me. Meanwhile she stops every colleague she passes: "Hey, wanna see this. It's really cool. It's a real Dupuytren's contracture." "What? Hmm, interesting, can I see?" My hand get massaged for the umpteenth time. "Does it hurt here, or there?" No it doesn't and I'm inclined to think it's a bad sign when you medical provider gathers all her colleagues to stare at you and they all exclaim "cool," or "interesting."

On the bright side, it has a name, it's real, I didn't make it up, and it's not neurological or psychological damage. Ok, I clarify: maybe there is some psychological damage, but it has nothing to do with my finger. And best of all, there are treatments possible, the doctor I'm being referred to will explain my options.

Having done some more research, I now know it's common among Northern Europeans (apparently very common among the Vikings). It occurs mostly in men in their 40s, by age 80 the women have caught up, and it's equally common in women and men. Just my luck huh? A woman under 40, without any of the risk factors it's associated with, and instead of DC gradually introducing itself to me, it simply appears one Summer afternoon after my nap.


Picture source: http://orthoinfo.aaos.org/fact/thr_report.cfm?Thread_ID=140.

So I called my mother. I hadn't talked to her in a week or so. "Ma, have you ever heard of Dupuytren's contracture?" Expecting her to say "what?" I was surprised when she said "well you're father had that on his foot, and so did his sister. They both had surgery for that a few years ago." I vaguely remember my father having surgery on his foot a while ago, but had had no clue what it had been about. Was someone going to bother telling me that this thing ran in my family? I told her I had it in my hand, and described the symptoms. "Oh," my mom replies. "I've had the very same thing happen to my hand the past 2 years. It keeps on getting worse. I just thought it was some kind of muscle thing related to aging."

Double whammy. I'm getting it from both sides. Both my parents had nice gradual introductions to this affliction, but since Germanic ancestors from both my parent's side fooled around with those vikings, here I am all of a sudden with a ring finger refusing to stay in line and do what I tell it to. Note to self: give my kids plenty of advance warning.

So now, the waiting is for the hand surgeon to contact me. Although it's not painful, it's irritating as hell, because I forget about it, and I will reach for something only to realize I can't grab it, because I'm right-handed, and my right hand is less than 100% functional. It's also bloody inconvenient for doing any molecular biology, or microscopy. You kinda need your fingers to do itty bitty things that sometimes involves stretching the ring finger. I had never realized that particular detail before. But I'm painfully aware of it now. Oh well, maybe there'll be a quick and easy solution to this. Boring is good, boring is good, boring is good. At least they didn't accuse me of having pooped on the train.

Touchy

I mean Touch Screens. They do wonders for my little F1-2. And since he is in his new Kindergarten class with a grand total of 4 students and 2 computers, he is been exploring the world of software for children with disabilities like never before. He seems to really like the software called "The Letter Machine" by Edmark. It uses a type-writer like interface on the screen, for the children to use the touch screen to touch a letter, which then results in cutsie pictures popping up and funny sounds. Perfect for F1-2. Now in December my parents (thanks!) purchased F1-2 a touch screen, but at that time he did not want to use the computer at home.

Now that we're in the final stages of re-constructing the kid's play area, the computer F1-2 used to use occasionally, has been taken over permanently by F1-1. I gave my old laptop to F1-2, and now we have it set up for him. But darn it, the touch screen doesn't fit the laptop monitor!! A screen for the laptop monitor would cost me another $175, and that is money we simply cannot shell out right now. And F1-2 is constantly hanging around his laptop, wanting to play with it, but frustrated at the lack of touch screen. My heart aches for him. I guess we're going to have to find a way for to get him another touch screen.

My husband suggested trying to sell the old touch screen, but from the little research I did, it doesn't seem there is a big market for used touch screens. I doubt we'll get much out of that. And of course, if I do splurge and buy the kid the touch screen, how much do you want to bet that the 6-year old laptop finally keels over within the week?

Where is my son?

It's promising to become an uhmm...... interesting year. In the first week of F1-1's middle school years, we've gotten three complaints about him. One e-mail: he's really charismatic and funny, but I've had to talk to him twice already about being disruptive in class. This is what F1-1's favorite teacher writes me. Now, presumably, since this teacher is his favorite, he is on his best behavior in that class. Needless to say we're not off to a good start. Then another teacher called us on Sunday to complain about his being disruptive in class and lack of organizational skills. And this teacher overheard another teacher reprimanding F1-1, and told us to expect a third call.

Since then, I've watched every move F1-1 makes, but it's a little ridiculous. When is he growing up? I've emptied his backpack with him, organized all his class folders, thought him how to use his planner appropriately, had him do extra math exercises downloaded from the internet. I have to do so much with him, I suppose I'm in Middle School too. Except I've got my hormones under control, whereas F1-1's are starting to kick into full gear. Last week he came to show me his mustache, which, he claimed, needed shaving.

Yesterday went better (or so he says). Hopefully today will be better too. There is a bright spot at the horizon though. F1-1 has always hated reading. But two days ago he requested a novel for reading. The Da Vinci Code is not exactly written to 11-year olds, and my dear husband P1, was skeptical. I checked it out of the library for him, and he immediately read the first 3 chapters. Then, last night, when he was supposed to be asleep, I went into his room because the light was on. And he was still reading! Huh? Someone help! They stole my kid and replaced him with a fake!! I suppose that might explain the good behavior in school too.

Criticism does not equal libel

According to reports, PZ and SEED are being sued for libel by the author of a book that PZ reviewed. Not by any standard does the review that PZ wrote even come close to libel (there is nothing unjust about the post, and it does nothing to the author's reputation), so I can't imagine that the author has any legal leg to stand on. It might be that this is simply a stunt (as in: any press coverage is good press coverage), but it is certainly not making it any more likely that I would buy the book.

So, this post is in support of PZ, whose blog is the first and the last one I read every day. May you write many more book reviews, PZ.

Update: Blake Stacey has a timeline, and the details.

New schoolyear

This morning was the start of a new school year. An adventure for sure. With F1-1 starting middle school, and F1-2 starting Kindergarten, we have a lot of changes to deal with.

Needless to say the bus did not show up to pick up F1-2, so I had to take him in. Then quickly off to drop F1-3 at daycare, and then F1-1 to Middle School.

I think F1-2 will do well in his new class. His Kindergarten class is right next door to his pre-K clas, so it's almost like coming home. I was quite impressed to hear at the "meet-the-teacher" meeting on Friday that there are only 4 kids total in his "functional class room." Two Kindergarteners (of which F1-2 is one), and two 5th graders. They are all non-verbal, although the 5th graders are experts in using PECS. The class is lead by a teacher, two aids, and there is one intern. That makes the student-teacher ratio 1:1! Unless we move him out of the school, he will stay in the same class room through 5th grade. The focus will be on teaching him life skills like feeding himself, using the toilet, using PECS. He will also receive Physical, occupational, and speech therapy in group and individual sessions.

F1-1 did not want me to take him in, but I figured he'd be happier once he was in his home room without having to wander the halls endlessly in search of his home room. He walked several steps beside or behind me as if to say "I don't know this woman. I'm cool, and I don't need help." I tried to embarrass him as little as possible, and kept my distance.

What surprised me more than anything is how grown-up especially the 6th grade girls are. It's as if they all grew boobs over the Summer, and started wearing make-up and high heels. What happened to the little 5th grade kids I saw in the beginning of June? Will my son fit in with all these grown-ups. But I think he will do just fine. It's very interesting to watch pre-teen behavior. He ran into several kids he new and wordlessly hit his balled fist against theirs and turned his back on them without saying a word. I don't get it, but I think this must be an acceptable form of saying hello these days, because the other kids did the same thing and seemed nonplussed by my son's apparent lack of manners.

It's promising to be a very exciting year. Good luck to my both my big boys!!

Is America Ready for a Black President?

I don't like to post on politics in the US. It is not my country, and I feel I do not have the right. However, 2 of my children are US citizens and I do have the right to look out for their future prospects, and therefore, on behalf of F1-2 and F1-3, I speak out.

A couple of nights ago, I briefly saw a segment on tv titled: "Is America Ready for A Black President." I don't watch much tv, and I did not stick around for this, but the first thing that came to my mind was:

Because you feel the need to ask this question, the answer is probably "no."

Why is the color of someone's skin of any importance whatsoever with respect to his/her acceptability as a presidential candidate? Or their gender, their sexual orientation, their marital status. I can go on and on, but you get the point. The US is far behind other countries in the world, where men, women, and people of all possible skin colors are presidents, vice-presidents, cabinet ministers, members of parliament, and nobody thinks twice about it.

When I first came to the US, a colleague told me about a friend of hers, who had no idea what to fill in on a form when asked what her race was. She promptly filled out "human." On principal I never filled out those parts of questionnaires, I wouldn't know what to fill out. The whole concept of race is ludicrous to begin with, but even if I would accept US-accepted delineations of race, I still don't fit in any particular category, or more accurately, I would comfortably fit in all of them. So when the time came for me to be added to the pay-roll, I again declined to fill out the question of race. The form came back a few days later. I had to fill something out, or not get my paychecks. Surprised by this requirement I studied the form more closely. The options were something like: white, black, hispanic, asian, pacific islander, other. Aha! Other. I can live with that, I checked "other." The form came back again: You have to specify what your race is if you check "other." At my wits end I remembered the story my colleague had told me, and filled out "human." The form never came back.

Racism will persist, if people, governments and institutions continue to attach importance one way or the other to humans' physical appearance, sexual orientation, or other properties that have absolutely nothing to do with their ability to perform their functions. It's time to remove the sections of form that ask questions about race. In scientific terms there is no such thing as a race, it is a completely fabricated property assigned to humans that has no purpose other than continue discrimination.

The question: "Is America Ready for a Black President?" is inherently racist, and sadly, a reflection of a society not ready to discard racism.

Mind compartmentalization

A couple of nights ago, my husband and I were talking. My mother had just left and this was the first time in weeks that we actually had the time and the energy to have a normal conversation. He asked me if I think about my father a lot. And the answer is "no." At least not in the sense that I consciously sit (or stand, or walk) and think about times past all the time. But he is always with me, somewhere in the back of my mind. A constant presence. Like my brother. Both my brother and my father have their own little compartments in my mind where the have housed themselves, and make their presence always known, although not overbearingly so.

My husband told me he had never heard it described like that, so this may or may not be a common occurrence. My brother occupied his space shortly after he got ill, and he's been there comfortably ever since. My father moved in when he got sick a little less then two months ago. Initially my father tried to take over a rather large spot in there. Since I realize I have to move on and get things done, I cannot allow him so much room. Now the territorial battle seems to have subsided a little bit. He seems happy with the allotment of my brain assigned to him, and only occassionally does he come out and try to invade other parts of me mind. It will get less. We will settle down at some point and agree how much space he can take up.

Does this sound creepy? Considering that I'm a staunch atheist, there is nothing remotely religious about this concept, although it's easy for me to see that others with similar experiences may mistake this phenomenon as such. It's just a way to carry the people I love and lost with me, and remembering them without actually having to sit down and bring up specific memories. It's very comforting to me. Both my brother and father are always very close at hand. It keeps them alive, at least in my mind. All the time.

Welcome!

Good news this morning. My good friend and colleague M. and his wife R. went through quite the roller coaster ride over the last 9 months. But after successful IVF, and some ups and downs, their twins were born late last night (or early this morning, I'm not sure which). Welcome to the world O. and S. May you have a wonderful life!

Congratulations M. and R. Good luck with the parenting of twins and enjoy!

Update

My parent had been planning to visit me for months. When my father passed away, I convinced my mother to come anyway, which she did. She just left yesterday after a two-week visit. It was a good visit and my mother and I have never gotten along so well for such a long time. Unfortunately neither one of us felt much like doing typical vacation-style stuff.

I should have invited Knobody, her mother and father-in-law over, since they helped me out so much to get my mother's room ready on time. However, I think my mother wasn't up to meeting lots of new people and entertaining, and frankly, neither was I. We just spent a lot of time together, went out to lunch, and hung around the house. In the evenings and on the weekend she was busy with the kids, while I continued working on the construction project in the house.

I managed to get a pencil stuck in the roof of my mouth when I pulled the closet shelving system loose during install while I had the pencil in my mouth. Man, that hurt!! Of course, it was a great excuse to drink copious amounts of alcohol, after all, the wound needed to be disinfected.

The only major blunder for the past two weeks was that I booked my mom on a wrong flight out of here, and instead had to drive her to another airport to make her connecting flight home on time.

My apologies go out to Knobody, her mother A., and her FIL E. I had really intended to invite everyone over, but it just never materialized. Thanks again for all the help. I wouldn't have been able to do it without you!

Ma, thank you so much for coming. It was really good to have you here, and very therapeutic. You were great with the kids and a wonderful house guest. It was a pleasure having you and you're welcome anytime. After all, who will take F-3 aw-sci?

Trouble

Ok, I admit it. I'm having trouble starting up. And not just this blog. Everything. It seems strange that I would just have to move on as if nothing has happened when my life will never be the same. I'm unmotivated to continue my work, I have trouble concentrating, and I'm downright angry that I'm expected to just pick up the pieces and go on. When my brother died I was angry that the sun came up the next day. What I'm going through now is similar. I wash oping this blog would provide an outlet, but I've been unable to come up with topics to write on. I just got my new laptop last Monday. Shouldn't I be ecstatic to be able to use it for such a glorious purpose as posting on my blog. Even though my father will never read it? My boss left about 3 sticky notes with an article on my desk last week, and I only found it yesterday when I popped into the lab briefly. I have mountains of work to do and no drive.

Right now, I'm just hopeful that this rant will kick my ass into high gear and wake me up already. Will someone please help me out here?

P.S. construction project is in the final stages, and although hammering helps a lot, I'm still lacking motivation.

They've got to be kidding!

Really, this can't be real, can it? Actually, I know of one household that works exactly like that. And at least one member of this "partnership" thinks it is perfectly normal. Shivers up the spine.

How atheist in a minivan could even read to the end is a mystery to me. She must be very, very brave.

He lives on...

It seems strange to simply pick up your life where you left off after such a traumatic experience of going home to attend your father's cremation.

When my brother died, I was really angry that the sun came up the next day. How did the world dare to just go on as if nothing had happened? I felt guilty when I laughed for the first time again. How could I possibly find something funny? Although I don't feel quite as strongly now, it still is strange to move through the day doing the same things I did 3 weeks ago. Get up in the morning, get kids fed and ready, drop them off at various destinations, go to the lab, do science, chat with colleagues, have coffee, chat with colleagues, talk to advisor, chat with colleagues, have lunch, chat with colleagues, do a little more science, chat with colleagues, you get the idea: go through the day as if nothing has changed.

The trip wasn't easy. It was hard to get there (I still had to get a passport and a visa for F1-3), and it wasn't exactly easy to get back. I had to change my return flight to a later date. The time in between was mixed. It was good to be among family. My family is very close, especially in times of hardship, and I felt instantly, and completely at home. But I missed my father terribly. I kept on expecting him to walk through the door, or turn on the music.

A couple of the events surrounding our farewell to my father made the front page back home, and no matter where I went, there were always people recognizing my face or my name. They mean well, of course, but I shook almost a 1000 hands the day of the cremation already. I did get tired of it eventually. And my family members who stayed behind, probably still face the same thing on a daily basis.

I must say however, it was awe-inspiring to see how many lives were touched by my father, and how much of an impact he has had on my home country's society, and how much respect he's gained over the years. Maybe there were a fair number of people who appreciated him after all, maybe it wasn't all in vain. He does live on. Not only in the minds and the hearts of those he left behind, but also in the many projects and activities he was involved in. He does indeed live on...

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).

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.

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.

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:

>name-of-your-goi
ATGACGTGCAT......

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.

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.

Harvest

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.

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-APHIS SOD website
USDA-Forest Service Pest Alert
American Phytopathological Society News & Views