Dec 22, 2013

London's mold of doom

Before you travel to a new country you probably will hear a lot of things in advance: about the weather, the transport system, the language, the currency, or the myths and legends about how people are and the nuances of their culture. There are things however, you will never find out until you get there!

One of the most surprising things about London, perhaps the entire UK, is a black mold, a fungus so pervasive that nothing can escape it. It terrifies me because in my three decades of life I have not seen any life form so aggressive and resilient, besides Homo sapiens and cyanobacteria. I swear it! For the Brits it makes already part of their daily lives and their natural landscape, so they don't make a big deal of it, rarely mention it and seem to be pretty oblivious to its existence, but it is nonetheless one nasty fungus.

At the beginning of the autumn, when it was getting cold, I decided to wear one of my winter jackets for the first time in that season to go to the shop one Saturday morning, when I take a look at the jacket it had been completely colonized by the m****f***ing fungus. How disgusting, NAAASTY!

I had never experienced anything like it.

This fungus grows everywhere, it lives within a rubber that is used to seal tile corners in the shower and sinks, it grows within the fibers of the curtain shower, it grows within every wall where it probably feeds from the paint, it grows in pretty much every surface of any material you find in a house. It has completely invaded my flat-mate's shaving razor and she does not seem to realize it at all. I have seen this fungus in the lid of plastic lunch boxes from some people at work. It invades your clothing hanging in the closet if you leave it unattended for just a few weeks. It grew on the plastic lenses of a pair of 3D glasses I forgot in a drawer. The nasty fungus also thrives in the cold rooms of our laboratory and probably every laboratory in the UK, so it clearly loves the low temperatures and high humidity. Every so often, it needs to be bleached, but that will not stop it from invading once again! Nothing can escape this fungus of doom.

I must say that during the five years that I lived in Sweden, I never experienced a fungus like that in my apartment... not even during summer time. Neither in my hometown in Montería nor Bogotá I saw a mold so nasty, and that is the tropics! In Paris, I never had to worry about anything like this and the building where I first lived was probably a couple of hundred years old.

I have asked people around and I have seen other apartments and I'm sure this is not an isolated problem of my house, but a quite common occurrence. 

I think this has to do perhaps with the fact that the UK is an island, so the humidity in general is very high and the temperature rarely goes below freezing, at least in the south. Who knows.


Dec 11, 2013

Journey to myself - 23andMe, health results (Part 4)

I might have been one of the last customers of 23andMe to have received health information from the DNA sequencing service they offered. Although initially I was most interested in exploring my ancestry, the main reason I chose this service rather than any other ancestry service was because I could get the additional health information. Unfortunately, FDA has ordered 23andMe to stop providing health data and who-knows-when they will be able to do so again. As controversial as it is the interpretation of our individual genome data now, because we know so little, I think it is the right direction the world should move towards. Eventually, we should be able to access our genome data whenever we want, and have clear and extensive information of any risk for developing any diseases or condition before they have happened, so that we could act in advance before it is too late... at least if it is within the limits of our own possibilities and the available technologies. In an ideal world, this genome data should be used fairly for the improvement of people’s well-being, but it does raise concerns about whether ‘your genome’ becomes another product to be sold for profit, misused, and taken advantage of.

Several of my close relatives have died of cancer, my grandfather died of throat cancer, and three uncles have succumbed to different forms of the diseases before they reached sixty years old. So, I was very interested about what the results would tell me. I must say most of the results were totally unexpected.

23andMe provided Health information divided into four sections. These were: health risks (122 risk reports), inherited conditions (53 different ones), traits (60), and drug response (25). Depending on how much research has been done on the disease, condition, or trait, they calculate a confidence factor. If there is a lot of research done in the genetic basis of particular diseases, they mark it as four stars. If research has only been done in a very limited number of patients, they mark it with one star. For the health conditions which are marked with four stars a risk percentage is calculated, and this could be above average (higher risk), below average (lower risk), or average (typical risk).

In my report I was surprised to find that I have an above average risk for Coronary Heart Diseases (CHD). This is one of the diseases for which a lot of research has been done. Fifteen genetic markers have been identified over the years, and they show you in a plot which particular genetic markers you got and whether they are likely to increase or decrease your risk for the diseases (see the figure below). They have calculated that for men, the average risk of CHD is 46.8%; and this was calculated for men of European ethnicity. In their own words, “46.8 out of 100 men of European ethnicity will develop Coronary Heart Disease between the ages of 45 and 79”.

In my personal case, I was calculated to have 60.2% risk… meaning that 6 out of 10 people with my genetic markers will develop CHD. That is not a very positive prognosis!

Fuck genetics goddammit!

23andMe health results
My genetic markers for CHD, what is that large red bar? WHY TO ME!!!
For each genetic marker associated with the disease you will get an explanation of what it means, a summary of the research that it has been done specific for that marker, and you will be able to access further scientific literature in the matter. I think that is quite nice. 

In addition to CHD, I was calculated higher than average risk for a number of other health problems including type 2 diabetes, psoriasis, age-associated macular degeneration, atrial fibrillation, gout, and ulcerative colitis. I might say that my grand-mother had diabetes, and uncle suffers of gout, and on my dad’s side there has been a lot of “eye” related problems. My grandma’s sister became blind, my dad suffered retina detachment, and some of my aunts have undergone already eye surgeries for several eye-issues. Could that be related to my genetic markers for macular degeneration? Who can tell. As far as it concerns me, I should just take good care of myself and keep a healthy diet and lifestyle.

On the other hand, one of my “traits” results relates to Adiponectin levels, it says:

Adiponectin is a hormone that is secreted by fat cells. It regulates the breakdown of fats and sugars and influences the body's response to insulin. Lower levels of adiponectin may increase the odds of obesity while higher levels are thought to be beneficial and may reduce the risk of cardiovascular disease, type 2 diabetes, and related conditions. Many factors are likely to influence adiponectin levels, including genetics.

I was found to have two genetic markers that have been linked to higher levels of adiponectin, according to some research performed in Asian populations. So how will this affect my chances of CHD or diabetes remains to be seen!

Besides that, I was also found to have some genetic markers that have been associated to higher risk in other diseases, but the research is not extensive enough to calculate a risk percentage. Some scary examples are basal cell carcinoma, nasopharyngeal carcinoma, meningioma, and sarcoma. I also have some mutations that might increase my chances of developing bipolar disorder (funny).
On the positive side I was calculated to have a lower than average risk for Alzheimer’s, colorectal cancer, melanoma, rheumatoid arthritis, esophageal squamous cell carcinoma, stomach cancer, type 1 diabetes, among many others.

Another interesting part of the analysis is the drug response study. I was found to have higher than average sensitivity to a drug called Warfarin, and anticoagulant. It might also be that a drug called Clopidogrel will have lower efficacy in me... and funny enough this drug is used to treat CHD. They also found that I was a fast Caffeine metabolizer and I have higher odds of becoming addicted to heroin than average: oops, I better don’t try it out then.

On the traits part of the study I was found to have higher odds of detecting the smell of asparagus metabolites in pee. I don’t often eat asparagus so I can't tell you whether this is correct or not now, but perhaps I should add some asparagus into my healthy-heart menus. I also have mutations that gives me lower odds of developing chronic hepatitis B if infected with the virus, and I also learned that I have no resistant to HIV/AIDS or noroviruses, what a bummer!

I have one mutation that according to a study of 4405 individuals of European ancestry was associated with less freckling. I have another mutation that was found to be associated with typical number of freckles and moles in Anglo-Celtic people: how about freckles in Latinos?

On a more interesting note than freckling, I also have a mutation that gives me a “slightly increased episodic memory”, mutations that reduce my sensitivity to sweaty odors (lucky?), and I have a mutation that was linked to much less efficiency at learning to avoid errors, according to an study on 26 healthy German subjects. I also have the muscle performance of Usain Bolt and if I had been a woman, I may have had smaller than average tits.

Dec 5, 2013

Journey to myself - 23andMe, ancestry composition (Part 3)

I have finally gotten the full results of my ancestry, and as a good Latino I’m an extraordinary mix of peoples from all over the world.

53% of my genome is of European Ancestry, mostly Southern Europe: likely Spain but with a fraction of Ashkenazi Jew, which is a big surprise!

21.9% Native American! I so would like to know which tribes exactly. Hopefully, one day I could narrow my search to a particular Native American group.

5.3% Sub-Saharan African, mostly from West Africa. The health results also shows that I have the mutation that makes Africans great sprinters! I might give birth to the next 100 m World Record breaker.

0.5% North African or Middle Eastern, probably from my surprising Jewish ancestry.

And last but not least 19% unassigned awesomeness.

In conclusion, a true Colombian.

Dec 4, 2013

Journey to myself – 23andMe, ancestry results (Part 2)

So, who are we really? Where do we come from? It boggles me how little we know about our past and the history of our ancestors. How short our memories are to the point that we might know absolutely nothing about our great-grandparents. That is at least my case on either side of my family, I do not know who they were and where in Colombia they were from. Finally, today I started figuring out the surprising journey of my ancestors in the book of human evolution!

The results of my DNA sequencing are partially in! At the moment I only have information on my father's line through the Y chromosome, which is inherited only from men to sons; and from my mother's line through the mitochondrial DNA (mtDNA), which is inherited only from women to their daughters and sons. I have added links to relevant wikipedia pages where you can read more about things that may be hard to understand.

Y chromosome (paternal line)
On my paternal line, I am haplogroup E1b1b1c1a, which is a subgroup of haplogroup E1b1b1c. Most people who are E1b1b1c can trace their ancestry to the Near East (Iraq, Iran, Palestina, Jordan, Lebanon, Turkey) where it originated around 15000 years ago... that is about 500 generations ago, give or take. Sephardic and Ashkenazi Jews carry this haplogroup. However, people carrying this haplogroup are also found in North Africa (Egyptians, Algerians, Tunisians), where it entered in the 7th century AD with the Arab conquest.

E1b1b1c1 is rare in Europe but can be also found among populations bordering the Mediterranean Sea. According to the site around 5% of people in Sicily and Sardinia have it. It is also found at low levels on Corsica. It is also found in low levels in people from Portugal and Galicia, around 4% of the population. And it says in the website it could have gotten there from an early migration from the Near East immediately after the Ice Age or arrived with Sephardic Jews before the Spanish inquisition.

A few months ago I asked my father if he knew anything about the origin of his parents, he said that her mother had relatives who were of Jewish ancestry. According to the legend a group of about ten brothers, the ancestors of my grandmother, arrived at the Caribbean cost of Colombia sometime at the end of the XIX or beginning of the XX century. However, these results are from the Y chromosome, which does not originate from my dad's mother, but on his father side, which is then a bit mysterious.

This image shows the distribution of people with the haplogroup E1b1b1c1. The scale bar and colors are the percentage of people that in that region have that particular haplogroup. So in this case is no more than 20% of the population in any region of the world.

Mitochondrial DNA (maternal line)
In a previous post I had told you, dear reader, that about 90% of Colombian mestizos in certain regions of the country had mitochondrial DNA originating from Native American populations, according to some research, suggesting that some of the first Spanish settlers, mostly men, mated with the only women they could fine: Native American women. My results confirmed this, after sequencing 14% of my mitochondrial DNA I know for certain now that I had an ancestral Native American mother at some point (within the last 500 years), carrying the haplogroup A2.

Haplogroup A2 is common in Asia, Siberia, and the Americas. It originated 50000 years ago somewhere in China perhaps. It is found among 10% of Tibetans and other Chinese ethnic groups like the Dong and Yi people, and about in the same proportions in the Koreas and Japan. This might be why I like ramen and manga so much. About 90% of Eskimos have this haplogroup and this might explain why I felt so at home living in Sweden. It might also explain my extraordinary snowboarding talents.

It is also very widespread in Native American populations all the way from Canada to Perú and Brazil, but it is not found in the southernmost part of the continent, like Argentina or Chile. You find it in Mohawk, Navajos, Aztecs, Incas, and in about 50% of most Colombian Native American groups.

Map for the distribution of people with haplogroup A2. Black means that 100% of the native people in that region have that particular mtDNA.
Ice Maiden, an Inca mummy, also has haplogroup A2.
As I was saying, the results are not yet complete. I look forward to see the results from the other parts of the genome, so that I can check out the percentages of the different ethnic groups I am made from. The funny thing is that I never imagined one day I would create a folder in my computer named “My Genome” to store all my DNA sequences. That makes me happy.

In my next blog-post I will write about the health section of the results, so that you can see the kind of information this technology could give you. I found some extremely unexpected results, such as an absurdly high risk for Coronary Heart Disease. On the good side, I also found that I have a much lower risk of getting Alzheimer’s compared to the average person. It's a very detailed report so I may take a while before my next post.

See you next time!

Nov 10, 2013

London's dark side

Very often people ask me if Colombia is dangerous. Very often I hear people saying “I would love to go to Colombia, but isn't it dangerous?” And it is sad because let me tell you something, criminality in London town is pretty nasty. The things that I have heard and the things that I have experienced myself are hard to believe possible in the safe and peaceful continent of Europe...

A previous flatmate told me this story: he was on a taxi home after a night out, the taxi driver noticed he was drunk and charged him an outrageous amount that my flatmate refused to pay. Another taxi arrived and the two drivers threatened him with a knife to the neck! What?

Last Friday my workmate was in court witnessing the judgment and conviction of an 18 year-old boy that robbed him in the street. The boy tried to snatch my workmate's backpack, however he fought back. The boy escaped but the police managed to retrieve DNA samples from under my workmate's finger nails. Later on, this boy robbed some students and since they didn't have any cash, he forced them to go to an ATM and empty their bank accounts. Fortunately he was caught recently and was convicted to 4 years in jail.

The other day I saw a gang of about ten dudes beating up one guy, almost to death. I had to call the police... the police arrived and arrested some of them, the beaten up guy was taken to the hospital.

I don't know anyone in here that hasn't had their smart phones or bikes stolen at some point, but that's not unique to London, is it?

A year ago, a couple of days before New Year's Eve, I'm going to get some cash from an ATM machine a Saturday night... the ATM was saying “retrieve your card to get your cash”, I heard the card trying to exit but the card didn't pop out. After a few seconds the ATM displayed an “out of service” message and then rebooted, but the card didn't come out after all. I had a feeling that I was being a victim of crime. When I arrived home 30 minutes later, I went to my online banking to block the card, however I noticed that already some transactions had been made. I called the bank security phone-line and as I was reporting the theft I could see transactions being made with my card! I'm not sure how they did it but fortunately the bank blocked the card and gave me the money back the following Monday.

Big Beng
London is an amazing city and my time in here has been extremely positive, yet I can not help wondering whether at this point you really are safer in London than in Bogotá or any other descent place to live, as a matter of fact... it reveals how you are surrounded by people with corrupted hearts no matter where you go. You should always be cautious, it doesn't matter where you live. Nonetheless, never forget that the good people are the overwhelming majority of us Homo sapiens, regardless of all the violence we see in the news, the terrorist attacks, the murderers, the rapists, the corrupted governments...

When you hear in the news, Syria had chemical weapons... it wasn't Syria that had chemical weapons, it wasn't the loving mother who had the chemical weapons, it wasn't the man at the grocery shop that had the chemical weapons, it wasn't the kids at school that had them. It was a few mad men with power that had them. Those few men are not Syria.

When you hear in the news that Colombia is or was the biggest exporter of cocaine... it wasn't Colombia the exporter of cocaine, most of us 45 million Colombians had absolutely nothing to do with that. That was the thing of few evil or foolish men, corrupted and undeserving of being called Colombian. Those men and women are not Colombia.

Do not judge an entire population on the evil deeds of the few.

After all, the small acts of kindness that we do or experience everyday will not get any time on TV.

Nov 2, 2013

Journey to myself – 23andme, before DNA sequencing results (Part 1)

I feel that my life is about to change. I can not shake this feeling of excitement to finally and truly have genetic evidence of my roots. As a Colombian I am privileged to be racially mixed, within me rest the history of three branches of the human tree separated by many thousands of years of evolution and thousands of kilometers. I am the Native American, I am the men and woman that journeyed through Eurasia and ventured across the Bering Strait still through the ice age, fighting mammoth, frozen oceans and walls of ice 15000 years ago. I am the Spaniard conquistador, mounting horses and firing muskets, I am Cervantes and Don Quixote. I am the black slaves shipped from Africa, robbed of my humanity and retaken, I am cimarron and cumbia. I am a mix of Native American, Spanish, and African, both genetically and culturally, and I hope to confirm this with the genetic analysis.

My DNA ready to be shipped across the world

Previous genetic studies in Colombian mestizos have shown that we are about 60% Spanish, 30% Native American, and about 10% African... I have no reasons to believe I am different to that, but I am prepared for surprises. I want to find out if I can narrow my ancestry to a particular genetic group in Spain... is there a bit of North African in me due to the invasion of the Moors? What tribes of Colombia's Native Americans my Indian ancestry is from, is it Zenú, Embera, or Muisca? I may not get such detailed information, but I believe I have access to the raw DNA sequence data, so I may be able to do a few searches of my own.

Some Colombian families take pride in believing that they are 100% Spanish. Some other Colombian families reject their Spanish ancestry and express much hate because of the aftermath of the conquest. My families are a true example of this, on my mom's side they believe there is no Native American blood flowing through their veins and are outraged by the idea of a native ancestor. Many times I heard them take pride in the fact that in my grandfather's family there was a lot of inbreeding, they would say things like, “my dad last name was Londoño Londoño, we are pure Spanish, because they used to get married between cousins since they arrived to Colombia...” as if that was something good. On the other hand many times I heard my father express his despise for Spain, taking pride by saying that they have more facial features that resemble the Native American, and yet both mom and dad are unmistakably mestizos.

I am sure that if every child was aware of his or her true genetic ancestry, such kind of stupid believes that give rise to discrimination and oppression would not persist for centuries, as they have evidently persisted after hundreds of years since colonial times. This is particularly problematic when that kind of people achieve positions of power.

The other good thing about 23andme's service is that they will screen for my risk of developing some genetically inherited conditions or diseases, this range from lactose intolerance and boldness, to Alzheimer’s or Parkinson's, to some forms of cancer.

Very recently and very tragically my uncle (on my mom's side) passed away overcome by a rare form of cancer in his small intestine, he was only 52 years old. However, this is not the first time this has happened in my family, I already lost another uncle to prostate cancer and another one to liver cancer, both of them did not reach 60 years old. My grandfather (their dad) also died of cancer in the throat and it seemed that he lived as well with some form of skin cancer... he died around 75 years old or so. On my dad's side also an uncle died very young of lung cancer. So it makes me wonder whether I am at a higher risk for cancer than the average population, and whether I carry some bad mutations in my genome.

Thus, I can not wait until I have my results. Even if I am surprised with a higher risk of developing a severe disease later on in life, it is better to be mentally prepared even if there is nothing I can do. In any case, there is something I can always do, to enjoy every single second of this fragile life: fragile and ephemeral like evening dew and morning frost.

Oct 28, 2013

Not really quite what it looks like

Things are not what they seem. Look at this map from google... if you compare the relative size of the UK or France with that from Colombia, it looks like they are about the same size. France looks even a bit bigger. However, Colombia is 4.6 times larger than the UK in area and 1.6 times larger than France...

Area of Colombia: 1'138.910 km²
Area of the UK: 243.610 km²
Area of France: 675.843 km²

Now, while the UK is only 907 km from South to North (measured using Google Earth) and France 954 km, Colombia however is 1805 km long!!! WOW!!!

Or is it an optical illusion?

Not really quite what it looks like

Jun 23, 2013

A Madman's Diary by Lu Xun

This is the second book in my quest to read the best 100 books of all times. It is a short story published in 1918 by Lu Xun (1881-1936) and as in the previous book, I had not heard of the author before... and it surprises me to realize the extent of bias towards Western culture of my high school education, since in six years of literature classes at school back in Montería, I do not remember to have ever dealt with an author that was not Hispanic, American or European. The interesting thing about Lu Xun is that he was an innovator breaking from the traditional Chinese ways... and he must have been really brave to pull this off, in my opinion.

I must say that A Madman's Diary is hilarious! It is so uncommon to find a book that could actually make you burst into laughter. I could count a couple... I think it is really hard to be humorous in the written form; I mean, to the point of making you laugh out loud. All in all I rate this story very high, just for its entertaining value and without regard for its historical or literary context.

I do not want to give you any spoilers but the story is about this young man who thinks the entire world is full of cannibals, even his older brother is conspiring against him. Unfortunately for him, he IS their next meal!

Save the children...
Lu Xun

Jun 17, 2013

A Doll's House by Henrik Ibsen

I begin my journey to read the best 100 books according to the Norwegian Book Club. This list was compiled in 2002 by asking 100 authors from different countries to select their top 10 books and it is supposed to include books from all cultures and all times. I have decided to read them all in order to diminish my ignorance levels and become a better man. The list does not have a ranking so I decided to read them in alphabetical order by title, the first one being A Doll's House by Henrik Ibsen, published in 1879.

As of the day I saw the list for the first time I had never heard of neither A Doll's House nor of Mr. Ibsen. I must say this little book was a pleasant surprise. It is a play in three acts narrating the intriguing drama of a young married woman. It is not until the last act that you understand what this play is really about: a critic to society and the institution of marriage, in particular of women being oppressed, minimized, and underestimated by their husbands and society. In this case not really because of physical abuse but mostly because for her husband, she is just a pretty face with a vagina. It must have been extremely controversial when it was played for the first time, I wish I had been there.

As relevant then as it is today, unfortunately.

Exotic tulip

Feb 9, 2013

From Confucius to me

A few days ago I heard a Confucius quote on a TV show. Submerged in my own ignorance, I started wondering whether he really existed or not, if there was any evidence of his historicity. As I wikied him I learned that there is absolutely no doubts that he actually did exist, but that his genealogy is the largest and best documented of any person in the world. His genealogy includes about two million people after 83 generations and spanning more than 2500 years!

I thought, how cool it would be to know my own genealogy back 25 centuries or more: where would this take me? Back to the deep jungles of the Caribbean Andes, or to an ancient Iberian? Maybe somewhere else in the world far and remote, I mean, a lot can happen in 2500 years.

You could say that the first clue of my ancestry could be found in my last names, Cardona and Londoño. The Cardonas were a noble and old family from the times of Charlemagne. In the 8th century Raimundo Folch went to Cataluña to fight the Moors, and he did so well that Charlemagne made him Viscount and great Lord of the city of Girona, in the region of Cardona. The first Cardona in Colombia was José Solís y Folch de Cardona, who was a Spanish colonial administrator and viceroy of New Granada in mid 18th century, or that's what some people say on the internet. The Londoño last name is Basque and apparently it was some kind of small village. The first Londoños to arrive to Colombia during the late 17th century were the brothers Agustín and Juan de Londoño y Trasmiera. I think it's very unlike that I could trace my lineage directly to Raimundo, there are probably millions of Cardonas in Latin America alone. On the other hand, it's a bit more likely that on my mother side they could trace their genealogy to the first Londoño in Colombia; since they come from the same region were the originals settled down, a region called Antioquia. However, when I see myself in the mirror, I understand that very little or nothing can be told from my last names alone. I am a mix of races, part of me is Native American, part of me is from Spain, part of me might be African as well. Who were my Native American relatives? Which tribes in particular did they come from and which language did they speak? How long ago did it happen?

So I decided to look for genetic studies on Colombian populations to see if the level of mixture had been estimated before. I found a recent study in PLOS genetics published in 2008: Geographic Patterns of Genome Admixture in Latin American Mestizos, a paper lead by Colombian professor Andrés Ruiz Linares at University College London. They found that in a region of Colombia (coincidentally close to where my family comes from), people were roughly about 60% European, 30% Native American, and about 10% African. I should not be very different from that, I dare to say. The study also said that the majority of the mixture happened from Spanish men mating with Native American and African women. In another study I read that in the population of people from Antioquia the male Y chromosome is about 94% from Southern Spain, 5% African, and 1% Native American. On the other hand, the mithocondrial DNA, that is inherited only by mothers is in about 90% of the people Native American, identical to the Embera people.

My dad told me once, I'm not sure I remember correctly, that one of his grandmothers was nicknamed “la india”, because she might have been all Native American... if this is true, probably I have a higher percentage of Native American in me. My plan is to later on purchase the National Geographic service to find out my ancestry on both my mother's and father's side.

 This is my dad dressed as a Native American in one of his anthropological expeditions to the jungle