Tuesday, June 28, 2011

play my strings!

Right now world leading scientists are meeting at my old uni in Uppsala to discuss the latest in string theory. And we are invited to participate through a live stream;


Monday, June 27, 2011

My little pony helps explaining magic....

Science lessons can be found all around us, everywhere magic is happening and science is the tool that explains it. For example, science provides us with profound explanations of the magic happening in my little pony.
I am so jealous of this guy, I wished I had thought of this when I was in school. 

Monday, June 20, 2011

One flew over the cuckoo's nest, on acting and thinking outside "the box"

What does it mean, being crazy? I am not suprised that they have a hard time finding genes for various mental states.  I have met 30 doctors with my migrains, and they have not managed to "make the same analysis" and only one managed to make the right one. But certain "hard core" states are well defined, which means that we can help more people today.

Vintery, mintery, cutery, corn,
Apple seed and apple thorn,
Wire, briar, limber lock
Three geese in a flock
One flew East
One flew West
And one flew over the cuckoo's nest
 This is the rhyme that inspired the book and later the film "one flew over the cuckoo's nest" (according to wikipedia) about institutionalization of the human mind. You could say that mental illness and creativity does the opposite, deinsitutionlize it, liberates it. I might be the same neurological processes that are involved, and if so why is it expressed in different ways in different humans?
A study from my old “hood” Karolinska Institute studied the old myth; is there an association between mental disorders and creativity. 
The family study combined the Swedish registers and included 300 000 people with severe mental disorder. It was a so called nested case–control study which looked at the likelihood of holding a creative occupation in individuals who had received in-patient treatment for schizophrenia, bipolar disorder or unipolar depression between 1973 and 2003 and their relatives without such a diagnosis was compared with that of controls.
The results in the paper; “A familial cosegregation of both schizophrenia and bipolar disorder with creativity is suggested.” People with manodepression were overrepresented among those with creative jobs. They were also doing "very well" in their professions.
People that held “creative” jobs were found more often in families with mental disorders than in the controls. This indicate a biological process, but could also be environmental, after all families are like small countries with different cultures. Karin Bojs who reports in DN automatic exchanges creative person with genius.
I have a dualistic worldview. I see that imperfections are the drive for movement and evolution, and that this is true for every level of existence, from quantum mechanics, to cell biology, evolution and personal development. If things were perfect we would not exist cause there would be no motivation for movement and change. What some people judge as good other people judge as bad. The presence of cystic fibrosis gene in our gene pool is an example of that (see previous posting http://annabirgersdotter.blogspot.com/2011/06/i-am-mutant-and-i-am-proud.html)
It is chance and change, an ongoing process that is both aiding us and also creating diseases.
Creative states and the mental disorders are related. It is different expression of the same process, can we have one without the other? Can this be a hint of how people with mental disorders can be helped?  Is this something that can be manipulated with therapy?

I am just playing with the how future of psychiatry could look. Instead of trying to kill whatever processes we think are responsible, could their expressions be manipulated? I know people who rely on neuropharmacological treatment to be able to leave their house so I am not having a go at the medical industry (well maybe a bit). I am playing with the thought of instead of hitting what we want to kill, we could hit something that change how the process is expressed in the individual. Can it be supported and other pathways be manipulated...

Yes it is way out and probably wrong....outside the box...hmmm.....should I be worried?

No great genius has ever existed without some touch of madness.
says Aristotle.
The Image of Jack Nicholson comes from girlsonfilm.blogspot.com


Saturday, June 18, 2011

Do I need to include comic characters in order to get attention to my projects?

I have often wonder what it takes to convey an interest in science. In yesterday’s papers I got one clue.; Media do not care about scientific results unless it is 1) pointless 2) about comics. Yes I am choosing a negative  angle on it today.

Obelix making raw material for
scientific reports
Researchers have analyzed the injuries in the hilarious comic Asterix. Their results were great fun to read, they could tell which brain injuries the Romans had (and some Vikings, extraterrestrials and French) from looking at bruises and change in facial structures. Both “the big” Swedish papers DN and SVD reported this, as did the radio P1. That is amazing considering how little research that manage to get into the public eye.


Despite the entertaining read, I think it is sad that this is what the public gets access to. How much science has been reported so far in June?
I did a pubmed search.  Pubmed is a data base for published articles.
I found that 48089 articles were reported from June 1st to June 20.
48 000 articles, i.e. scientific reports, and the public gets to hear about Asterix injuries.  Why is this? No wonder the public doesn't know about E.Coli and how we use it to "grow" insulin, how DNA works, how bacteria can exchange DNA,  that we culture cancer cells to enable us to study the disease,  what nanotechnology is  and so forth.

And if I was the public, I would really question why scientists needed my tax money.

Thursday, June 16, 2011

In the future, will TV sets come with warning signs;"Watch with responsibility"?

The revolultion wont be televised. The author of these words  Gil Scott-Heron died in the end of May. Somehow it fits with the latest science reports on watching TV.
In Europe we watch TV 3 hours a day, Americans watch 5 hours a day. Western culture with all it’s amazing gifts have become more and more focused on “friction less living”. TV is a great tool to educate us and be used for catharsis and entertainment, but 5 hours a day? Now scientists are sure.
"Prolonged TV viewing is associated with increased risk of type 2 diabetes, cardiovascular disease, and all-cause mortality.”
 3-5 hours a day is prolonged viewing, we are killing ourselves. TV is a drug. If we can forbid and limit access to drugs and alcohol because it serves the  interest of the citizens and their health, why should there be a TV in every house? The drugs, just like TV holds promise of entertainment and aiding good health and catharsis at a  limited use (I am not saying that we should do drugs, I have seen firsthand how it can kill and destroy people so I would be the first to suggest caution).
Why  should we have a TV in every flat, when we are not allowed to access alcohol or drugs with the same convenience because of the possible danger they posses? Why are some drugs ok? I am just looking at the data, I am not advocating the use or non-use of drugs. Almost everybody is a druggie...we just use different drugs to numb ourselves or liberate ourselves from whatever is going on in our lives. In the future, will the TV come with a warning note, just like cigarettes does now? "Watch with caution, Watching might kill you, Don't watch with your children".

I don’t have a TV myself, I threw it out after I started to follow Big brother ten years ago. That was for me the lowest of the low. First I wanted to throw a party with the theme “throw the TV out of the window” but to my neighbor’s (unknowing) happiness I did not.

Scientists did a meta analysis (that is they gathered all published data from way back in 1970 up to today and put it together) and proved that watching TV will kill you by leading an earlier death.
I wonder if you add it all up, the computerized workplace, the commuting by cars and trains, will the TV stand out as the sole “killer”. Computers do play a bigger role today in our everyday lives. Perhaps these new computer games with movement sensors and such will change this.

The Disposable heroes of hiphoprisy raps; TV the drug of the nation.

This is from the paper;

“8 studies included, 4 reported results on type 2 diabetes (175 938 individuals; 6428 incident cases during 1.1 million person-years of follow-up), 4 reported on fatal or nonfatal cardiovascular disease (34 253 individuals; 1052 incident cases), and 3 reported on all-cause mortality (26 509 individuals; 1879 deaths during 202 353 person-years of follow-up). The pooled relative risks per 2 hours of TV viewing per day were 1.20 (95% CI, 1.14-1.27) for type 2 diabetes, 1.15 (95% CI, 1.06-1.23) for fatal or nonfatal cardiovascular disease, and 1.13 (95% CI, 1.07-1.18) for all-cause mortality. While the associations between time spent viewing TV and risk of type 2 diabetes and cardiovascular disease were linear, the risk of all-cause mortality appeared to increase with TV viewing duration of greater than 3 hours per day. The estimated absolute risk differences per every 2 hours of TV viewing per day were 176 cases of type 2 diabetes per 100 000 individuals per year, 38 cases of fatal cardiovascular disease per 100 000 individuals per year, and 104 deaths for all-cause mortality per 100 000 individuals per year.”


Wednesday, June 15, 2011

I am a mutant and I am proud!

This post is about tracking the "origin" of human mutation and calculating it's rate!

In a scene in X-men 2,  a mother exclaim “this is all my fault” when discovering that her son is a mutant. The reply is “Actually , they discovered that it is the male that carries the mutant gene, so it is his fault”, refering to the father.

J.B.S. Haldane proposed in already in 1947 that the male germline may be more mutagenic than the female germline. Diverse studies have supported Haldane’s contention of a higher average mutation rate in the male germline in a variety of mammals, including humans. We can explain it theoretically.

A woman’s eggs are created while she is a fetus inside her mothers womb. 50% of my blueprint originated from the time when my mum was “baking” inside her mother’s i.e. my grandmother’s womb. Once a girl reach puberty her eggs mature, but they were there all along. The meiosis took place when she was a feturs. Meiosis is the process that makes germ cells. It is a cell division that produces cells with half the gene content.
Men have meiosis all the time, they make new germ cells during their whole life cycle. Children that have elderly fathers have a higher risk to develop autism. The hypothesised cause has been the increased mutations found in sperms, as the cells producing them accumulate more and more mutations.
Men thus might be responsible for increasing the rate of mutations in humans. It is not  necessarliy bad. It increases the risk of some diseases yes. But it also increases the chance of survival. Genetic heterogenity is the basis for evolution. http://annabirgersdotter.blogspot.com/2011/01/your-body-is-constant-change-everything.html 
In this post I wrote about biological change constantly taking place in the body. Change is constant on every level in nature. That is why survival is partly dependent on plasticity and change. We are all mutants, although it is not expressing itself like in X-men.
Mitosis is the common cell division that produces two cells with the exact same gene content i.e. 46 chromosomes. But do the two cells have the EXACT same DNA? No.
Watson and Crick wrote, “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” The balance between correct and incorrect DNA synthesis is relevant to evolution of the species and to the health of the individual.

When a cell is going to divide it replicates it’s DNA i.e. it makes a copy. The protein that reads the mother strand and creates a daughter strand is called DNA polymerase. It is not 100% correct.  There are proofreading systems that correct errors/mutations (that might also be caused by ultraviolet light, chemicals, deamination of methylated cytosines etc.) but these are not 100% correct either. The system is slightly leaky. This is how mutations are caused.
(There are several ways that the genetic code can change, not just through the error of DNA polymerase.) It is the same process in mitosis as in meiosis.

Is it true that more mutations are inherited through the father?
Nature recently published the first direct comparative analysis of male and female germline mutation rates from the complete genome sequences of two parent-offspring trios. The work is extensive. And the paper reports;
“Most strikingly, in one family, we observed that 92% of germline DNMs were from the paternal germline, whereas, in contrast, in the other family, 64% of DNMs were from the maternal germline. These observations suggest considerable variation in mutation rates within and between families”*
Thus the male germline contribution was responsible for the vast majority of mutations in one family as expected but not in the other. As always, science seems to need more data and larger cohorts. The study suggest considerable variation in mutation rates within and between families, which is really cool!

Why would we want to know more about mutational rates and how they are carried along the ancestral lines? One reason is that a more precise estimate of human mutational rates will help us understand evolution and help us understand how we could use DNA sequencing technology to increase knowledge in that field.

What is a mutation and what is genetic variation? I am myself a bit bewildered at this point, as scientists seem to use the word freely. Is mutation bad? Could be both. A buddist answer is that nothing is good or bad, it is what it is. The current environment decides what fits and does not fit.
One example is the cystic fibrosis gene. Cystic Fibrorsis (CF) a genetic disease that is too common in the European population for it to be there by chance. That means that at some point, to carry the gene gave a survival advantage. If you are homozygote (i.e. inherit the gene from both your mother and your father) you will die from bacterial infection as the lungs won’t be able to deal with the mucus production. It has been suggested that if you live in an environment where you are subjected to diseases that cause the body to secret fluid, people that were heterozygote for CF were better at keeping fluid in the body. They would have an advantage to survive in periods of dysentery.  

Another example showing that it is not necessary bad to have genetic variations/mutations is the famous 32 base deletion of CCR5. CCR5 is a chemokine receptor and it is one of the receptors that aids HIV uses to enter the cell. It confers resistance to HIV infection. This is common among people of nothern European descent at a higher degree than one would expect. The hypothesized explanation in this case is that people with the deletion had resistance to the bubonic plague (that took place in 1350 very approximately). This mutation is not present in Southern Africa and they never had the plague. Another theory suggests that the selective pressure was caused by smallpox.

So be a proud mutant, you might carry the survival of your offspring in those faulty genes!
And yes, I only wrote this post so that I could download images of Wolverine!



Galvani A, Slatkin M (2003). "Evaluating plague and smallpox as historical selective pressures for the CCR5-Δ32 HIV-resistance allele". Proc Natl Acad Sci USA 100 (25): 15276–9. doi:10.1073/pnas.2435085100. PMC 299980. PMID 14645720.

Sunday, June 12, 2011

Feeling hot hot hot?

Saw this in an interesting blog and basically copied it...

Scientists agreeing that global warming is caused mostly by human activities:

Percentage of climate scientists agreeing: 97.4
 Percentage of meteorologists agreeing: 64
 Percentage of economic geologists agreeing: 47

Americans in general  answer the question; estimate the no of climate scientists that claim that global warming is caused mostly by human activities;

81 to 100 % climate scientists claim etc —        15 % (of Americans)
 61 to 80 % —                                                     18 %
 41 to 60 % —                                                     18 %
 21 to 40 % —                                                     12 %
 0 to 20 % —                                                         7 %
 Don’t know enough to say —                             32 %

Somehow this would be an example where information has failed to come through?


Blog I knicked it from;


Tuesday, June 7, 2011

Get to know the elements

Crazy British Scientists have made a very nice overview of the periodic table in the form of short films. I say crazy cause they went to Ytterby in the middle of the winter. But then again, I went to Birmingham to do research, who is more crazy? :P


Domestication of microbes.

Just like we once domesticated cows, sheeps and dogs because it eased our living, we have now domesticated microbes. Our new household animals include yeast. Yeast was the first microbe to be domesticated as man discovered bread baking and beer production.

The domesticated E.Coli is the biggest hit so far. It is easy to cultivate and is harmless (most of the time). E.Coli has been used to produce therapies like insulin, antibiotics, enzymes, vaccines and so forth. The world as we know it would cease to exist if we took out E.Coli out of the equation.
If we look at our future big hits with microbes, what would they be? Microbes might be used to degrade pesticides. Viruses might also be used instead of pesticides killing off insects. Just as in Turkey, where the king hired Vikings to fight of the attacks of other Vikings, nice fungi might be used to fight of bad fungi.
There are microbes that feed on oil that could be used to clean up big oil spills. Some microbes can produce light. Kits are being developed to use microbes to analyze pollution in water. The health industry is on the track, producing drinks with “nice” microbe strains.
Could they in the future be included in beauty products? “Hey wait a minute, I need to viral spray my hair”. "Where is my microbe cream?" Why not? I am sure there is a bacteria that feed on wrinkles J


Monday, June 6, 2011

A breif history of our dependence on E.Coli (or why is E.Coli not a totem animal)

As everybody else, I will write a few words on the enterohemoharric E.coli  (EHEC) outbreak. E.Coli or Escherichia Coli is in general a very nice helpfull guy. 

I have played with the ancient/new age idea of totem animals and how they seldom include the really cool animals such as viruses and microbes. I would like to add EBV as my totem animal. But E.Coli is not a bad totem animal either. It has helped humanity tremendously; it is like the modern day horse. The world would look different without it.E. Coli have been cultured and harvest in labs for almost 100 years. Without E. Coli biotechnology as we know it would not exist. E. Coli is used to culture and harvest proteins that we depend upon for health. This includes insulin antibiotics, vaccines and many other therapies. 

E.Coli producing insulin

The benefits of E.Coli does not end there. James Liao of the University of California (UCLA) have developed a way to produce normal butanol using E. Coli. Butanol might be a greener alternative to gasoline.
E. Coli's more imaginative applications include by inserting genes that produce light, it has been used to make primitive cameras.

As I wrote in earlier postings, we have an abundance of bacteria living in harmony inside us and E.Coli is one of them.
We are colonized from the moment we take our first breath and this is a good thing. We depend on the bacteria to take up space and compete out dangerous organisms.
How is that for a totem animal, it can be used for the benefits for all and the individual depends on it for good health and we are in constant interaction with it?

It is a universal truth and thus includes bacteria, E. Coli comes with a constructive and destructive possibility. E. Coli have been the villain in epidemics . What we see now is on its way to become the biggest outbreak in history with approximately (so far) 1,730 infections and 18 deaths. The bad version of  E.Coli carries genes for a poison known as Shiga toxin ( dubbed after Japanese bacteriologist Kiyoshi Shiga).It halts protein synthesis in cells.

The villain in the recent outbreak is called strain O104:H4. This strain contain segments of DNA not seen in other E. coli strains. The new DNA is hypothesized to be responsible for the high level of virulence. To make things worse, the O104:H4 strain has even acquired new genes that make them resistant to antibiotics. It is the darth vader of bacteria.

The life cycle looks like this; The microbes  get into vegetables through manure-laced irrigation water. In the large intestine, they insert molecular needles into gut cells and inject molecules causing the cells to dump out nutrients for the bacteria to feed on.


Sunday, June 5, 2011

30 years ago we "discovered" AIDS

This will be a personal text.

The first AIDS case was reported 30 years ago. I was seven years old. I did not hear about the disease until three-four years later.
In 1987, my school was contacted by the arty Swedish Film director Roy Andersson. He had been hired by the Swedish state to make an information film about HIV and AIDS. A suprising choice
He wanted to show what the future might look like if we continued the path of fear. Fear of the virus, fear of sex, fear of being vunerable in the face of disease. So he created a dark school scene where young girls were taught have to use a condom under teacher's "it is all natural, dont you dare think anything else" supervision.

The scene is hilarious. Remember that we were twelve, it took hours before we stoped laughing and they could actually do the shooting. Luckily Roy's vision is wrong. We are not that afraid as he visioned us to be. The dark futuristic condom school scene starts at 1.56 and ends at 3.17 approx. I am in the back second row from the right.


Saturday, June 4, 2011

It is never to late to change your mind; how to make a neuron from a skin cell

The take home message from Kung Fu panda 2 (the kaboom of doom) is; your history is not important, it is who you choose to be in the present that count.
I have written several posts about the changing of cells in our bodies. The stem cells divides constantly, providing cells to our organs. But the cell need to differentiate, which means that it has to take step by step changes in order to end up as with a specific phenotype (cells as energetic stable states and their malignant counterpart is presented in review below). This specific phenotype, which we scientists like to refer to as lineage commitment, is robust.
I will write more about stem cell therapy in another post, it is a therapeutic possibility that sparks the imagination. The stem cell is tabula rasa. It has the promise to become any cell from a wide spectrum of choices. For every step it takes, it comes more specialized, and thus the range of choice decreases.

Image taken from the nature publication
showing a former
skin cell working as a neuron

In this post I am focusing on dedifferentiation/transdifferentitation. Once the cell has ended up with a specific phenotype, can it go back? If it can change, which programs are available? Can it backtrack and become any other cell in the body? The cloning of Dolly proved once and for all that every cell in the body has the same genetic set up and in theory could be used as a template for any cell type. Or is the cell’s end-phenotype stable and the only differentiation that is available to it is malignant progression? This last interpretation would fit with western linear thinking and perception of time. Previously I did not believe in dedifferentiation, I thought that the amount of energy that went into driving a cell from tabula rasa into an individual was too costly. I compared it with me not being able to go back in time and become 25 again (it hurts doesn’t it? J )
If we could take a cell, any cell from you, and get it to change it’s phenotype (which means it’s characteristics and it’s history), we would be fulfilling all the promise of stem cell therapy and beyond. I would like to write about this in parallel with eastern spiritual teachings. Not as a truth but just to “spice” it up. According to eastern spiritual teachings there is only now, history and the future is interpretation and ideas of the mind in the present. Now what if we can apply this to cells?
Can a skin cell become a say a heart cell or a neuron, does transdifferentation really exist?
The answer is yes. In the past year, researchers have converted connective tissue cells (fibroblasts) found in skin into heart cells, blood cells and liver cells. Transdifferentiation does not occur naturally (luckily or we would all look like we belonged in a H.P lovecraft novel), we need to give the cell a little help.
Now to the science parts; fibroblasts exist in various forms in every organ. By introducing transcription factors Gata4, Mef2c, and Tbx5 into the cells, scientists reprogrammed postnatal cardiac or dermal fibroblasts directly into differentiated cardiomyocyte-like cells. Induced cardiomyocytes expressed cardiac-specific markers, had a global gene expression profile similar to cardiomyocytes, and contracted spontaneously. Thus fibroblasts from skin can be used as a therapeutic pool for mending “a broken heart”. They can also be used to mend “a broken mind”;introducing factors Ascl1, Brn2 (also called Pou3f2) and Myt1l, converted mouse embryonic and postnatal fibroblasts into functional neurons in vitro (this means outside the body).
How cool is that? Lineage commitment (cell differentiation) is not written in stone. It can change. We can change linage commitment by giving it a kick. I like to think that we work in the same way. We take so much for granted and sometimes things happen in our lives and we are forced to reinterpet the meaning of life, relationships, money and love. Some time or another, most of us live through a transdifferentitation.
Pang, Z. P. et al. Nature advance online publication doi:10.1038/nature10202 (2011).
Reveiw; http://www.ncbi.nlm.nih.gov/pubmed?term=ernberg%2C%20kauffman