Monthly Archives: December 2008

Human inbreeding: examples

In a genetics class I attended recently, Professor Scott Weitze recommended a few books including The Family That Could Not Sleep by D.T. Max and Mutants: On genetic Variety and the Human Body by Armand Marie Leroi. I thought I should mention both these books because both deal with mutations that probably arose due to human inbreeding.

The Family… lists many prion related symptoms which seem interesting from the perspective of inbreeding. The Italian family referred to in the title is haunted by progressive insomnia that kills the victims within months due to sleep deprivation. Although this condition is due to prions, the fact that this condition is inherited makes me believe that some inbreeding may be involved. A mutation that promotes the incorrect folding of the protein which creates the prions may have arisen in an ancestor in the family. Due to consanguineous marriages the incidence of the mutation may have increased to the current status within the family. Mutants, too, is a wonderful book that links myth, reported cases, and medical cases of human deformities that have lingered since ancient ages.

While The Family…. consists of many prion related diseases, Mutants starts with the description of the mythical Monster of Ravenna that remarkably resembles patients with Roberts’s Syndrome. Then leading the readers from the battle of preformationists and epigeneticists the book delves into the modern day developmental biology to explain various irregularities during the development of an embryo that leads to deformities. While some developmental irregularities could be due to the environment and chemical agents, others such as ectrodacytly (previously also known as Cleppie Bells or lobster claws) could be due to inbreeding because they seem to be in the individuals that seem to have shared ancestors. Cleppie Bells in a few Scots family, Lobster claws in a British family, Ostrich foot in an African family, and the aleijadinhos of Brazil are some of the examples of ectrodacytly listed by the author. All these deformities are in very small populations sharing a common ancestor. I thought this would probably be interesting especially to those who refute the negative implications of consanguineous marriage.

I would not want to summarize the books because the authors have spent a lot of time and effort to write them. I would suggest though that readers interested in deciphering more about the implications of human inbreeding read both of these books.



Filed under Human Evolution

Human inbreeding: the logic behind it

Earlier in this blog I have written twice about human inbreeding. I never thought that my writing would attract so much attention. The first article, a compilation of a few readily available scientific papers and possibly a few articles in Google, was my effortless entry to the blogosphere. The attention I received inspired me to delve into this issue even more which brought about the second article, which comprised of considerable archeological excavation of scientific literature. I appreciate all the comments that readers have provided. I can only hope, whether you agree or disagree with me, that my articles have furthered your understanding of human inbreeding.

Many of the readers who cared to express their disagreement with me mentioned that even though the entire royals of UK, the Japanese Monarchs, and the ancient Egyptian royals are products of inbreeding, they do not show any aberrations. In case of British Royals, hemophilia may not have been due to inbreeding as another author pointed out. Yet another reader giving her own example said that despite being inbred, her brother and she are fine “just like everybody else.” I completely agree with these arguments and arguments like these that just because one is descended from a consanguineous marriage, one may not show any aberrations. However, one should always consider that there may be recessive lethal mutations in us and the probability of such mutations being passed on is highly increased in consanguineous marriage.

For example, assume there is a gene P that is vital for life. In any population, because of mutations there can be various versions of gene P. Let us assume that there are three functional versions P, P’, and P.” The fourth version p let us assume is deleterious and recessive. All four alleles are distributed equally. From this description, individuals with genotype PP, PP’, PP”, P’P” are fully functional whereas Pp, P’p, P”p are carriers and pp individuals show symptoms. In this population, the allele frequency for p is 1/4 and the chances of one being pp is 1/10. This means that the probability of a person showing the mutation is 10%. Now let us assume that in this population there is a family in which a son (or a daughter) has the recessive deleterious allele p such that his genotype is –p (it does not matter what his other allele is. Thus, the functional alleles are indicated by a dash). Assuming his wife had two of the functional alleles –, the chances of his children inheriting the allele p is 1/2 (in the population the risk was 1/4) and the chances of pp individuals are 0. Let us assume he had for children with the following genotype:–, -p, –, -p. If the kids with –p genotype marry with people of — genotype, then the chances of
-p individuals in next generation is again 1/4 and the same for pp 0 but if they get married together the chances of –p is 1/2 and now the probability of pp individuals is 1/4 which is 25% that is 15% higher than the general population. This is where inbreeding matters.

Now having that said, there are a few things that we need to consider before discussing the effects of inbreeding. First, only the mutations that can be seriously detrimental can be easily reported and measured. If one is a carrier (-p genotype) it becomes harder to characterize them. Second, if the mutations are in the genes that are important but not life threatening, the individuals carrying the mutations may appear normal. These mutations include genes responsible for eye colors and hair colors. Third, some fetuses carrying detrimental mutations can result in miscarriages and stillborn babies and those that live may only last for a few years. We only know about the mutations in famous people and those in general public may not be known. Therefore, although the royals may be inbred yet okay, we cannot assume that inbreeding is okay.


Filed under Evolution, Human Evolution

Who killed Madan Bhandari?

madan bhandari


Filed under Nepal, News from Nepal

AIDS: a photographer’s and an economist’s perspectives

There is so much information about HIV/AIDS in the net but still this pandemic is on the rise. I tried to explain what a conventional website such as Wikipedia does not tell you about HIV/AIDS in my previous article. I am including a few links here to assist you better understand the havoc it has caused. The second link is an economist’s perspective on HIV. It is a very different thinking about the pandemic, none like I have ever heard before.

A Photographer’s perspective: A short talk accompanied by photographs of Kristen Ashburn

An Economist’s perspective: Emily Oster on AIDS in Africa

(Materials were obtained from TED)

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Filed under My Life My Thoughts

HIV/AIDS: What the Wikipedia does not tell you

The Chinese name their years after animals. There are years of the dogs, lions and even dragons. From that perspective, the year 2008 was the year of the viruses. If the naming was to be based on the Nobel Prize in Medicine, one half of which was awarded to “Harald zur Hausen for his discovery of “human papilloma viruses causing cervical cancer” and the other half jointly to Françoise Barré-Sinoussi and Luc Montagnier for their discovery of “human immunodeficiency virus””.

Not only this year but also the last few decades probably can be considered “the decades of viruses.” In fact, particularly of one virus– HIV, for all the havoc it has caused worldwide. Despite the billions of dollars spent and thousands of scientists, sociologists, and medical personnels working desperately under the pressure of high competition (in case of scientists) there is no cure for HIV. Many attempts to make vaccines have failed and scientists are back to the drawing board to tackle this menace. If there were a riddle for HIV, it would probably sound like this:

Its only me, its only me,
Millions of men are carrying me,
Millions more have been killed by me,
Thousands of men are chasing me,
Two decades of studying,
No cure from the wraths of me,
Its only me, its only me!

This riddle I just made…if I were to ask Gollum this riddle he probably would not know…but it still probably is barely mediocre…and that’s why I have a day job. In fact, I am one of those thousands of men chasing the HIV. For the last two years I have worked in HIV research and so, I am ebullient to jot down my thoughts despite the fact that I am no expert. A good review of HIV encompassing its history up to the treatment can be found in Wikipedia. I am only going to tell you about a few things that you cannot find in Wikipedia and some recent development in HIV research. If anyone is interested in finding any sort of detailed statistics on HIV you can visit the UNAIDS/WHO Global HIV/AIDS Online Database


There were a bunch of historical essays published in the journal Science (29 Nov, 2002 issue) two of which are particularly interesting from the context of HIV discovery. The first essay is written by Luc Montagnier, one of the Nobel awardees, who describes the first hand experience of discovering the HIV in his lab. This article is followed by another essay by Robert Gallo. It sucks that such prominent journals like science is not accessible to the public but pornography is. That tells a lot about why kids are not interested in science….the lower case ‘s’.

Anyway, although the Nobel was awarded to the French discoverers, the first two retroviruses (HTLV-I and HTLV-II) were indeed, discovered in Gallo’s lab in the USA. Furthermore, there was also some collaboration between these two groups while investigating the HIV but later the collaboration ended when Gallo discarded a joint conference scheduled between his lab and Montagnier’s lab to side with the US government to claim the discovery first and to develop the patent rights and totally forgot his French collaborators. Gallo did not have the world “loyalty” in his dictionary.

In his Science essay Gallo puts all the blame on an unnamed freelance journalist and U.S. Dept of Health and Human Services Secretary Margaret Heckler. “The scientific achievements were overshadowed by a dispute between the United States and France over the patent rights to the blood test, and a temporary disagreement among the scientists,” Gallo says in the paper. That keeps me wondering why he did not mention the French group in that press conference. Was he trying to hoard all the glory to himself? Or may be he credited the group and still there was a controversy? Only Gallo or Heckler knows. This suggests there can be…I correct myself….there are bigger dramas in scientific world than Hollywood itself!

Who discovered HIV is probably a mute point now except for the glory of Nobel and a relatively small and insignificant amount of $$ from the Nobel group…yes it is insignificant for the achievement of a lifetime…even failing car company CEOs get ten times that EACH YEAR! In the real world no one cares about who discovered it. Do you? I don’t. But there is a growing curiosity in everyone because HIV is no longer limited to Africa or to the gay community. It can infect anyone.

HIV has severely affected sub-Saharan Africa where it continues to be the leading cause of death. Lack of knowledge and lack of a social support system has lead to the modern day pandemic of HIV. In an article in August 9, 2008 issue of The Lancet, Merson et al. wrote a very good and comprehensive summary of history of HIV and how the lack of knowledge and social support system has fueled the pandemic. Even though HIV pandemic was recognized in 1981 (that was 27 years ago!) by the US Centers of Disease Control, everyone thought it was limited to gay men and peoples of the third world living in penury. Most of the world and their political and religious leaders were in denial of the fact that HIV was spreading in an unprecedented rate. To know more about HIV’s history and about social issues related to HIV two papers are a must read: Merson et al. and Gupta et al., both published on the Lancet (vol. 372, August 30, 2008)

While the leaders turned their back to the pandemic, a few people took it into their hands to start some social support programs to ameliorate the pandemic. In 1982, Bay Area Physicians for Human Rights, a San Francisco doctors group, were the first to issue education materials to the general public. Their efforts were followed by many local and international agencies in various parts of the US, South America, Europe and Africa which condemned prejudice against the HIV infected people and initiated a social network to provide care and support for the HIV infected patients. It was only in 1987 that WHO launched its Global Program on AIDS (GPA) which reached out to every single constituencies including activists, community groups, NGOs, and HIV/AIDS patients. GPA was shortly replaced by UNAIDS. Despite the increasing efforts of UNAIDS and other organizations, worldwide prevention efforts have not been sufficient to reduce the HIV infection rates.


Sadly, despite so much literature on how is it transferred there is still a huge void on people’s understanding of how HIV is transferred. “Oral sex is safe; it’s only vaginal sex and anal sex (men are screwed both ways) that HIV is transferred.” “Using condoms can prevent HIV.” “Magic Johnson is doing okay with HIV. Why can’ I even if I were to be infected?” “There are antiretroviral (ART) drugs now and there will be vaccines in near future.” All these are fallacies. No unprotected sex is safe, INCLUDING ORAL SEX. There will soon be papers that will demonstrate this fact. Condoms do not provide 100% protection either. One can be on ART and live long like Magic but ART does not work on everyone and there are thousands who fail ART treatment. Even if the treatment is successful one is not cured and will have to endure a lot of hassles just to live. Can you imagine being sick all the time, contracting flu every season, contracting bacterial and fungal infection easily? How about the possibility that you may not be able to have a kid? Life with HIV is very grim so the best way to prevent it is to stay safe.

Two decades have passed and there is yet no cure for HIV. Merck was probably the closest to developing a vaccine but the failure of STEP, the Merck vaccine trial, was such a big blow not only to Merck but to the entire scientific world that they have returned back to the drawing boards. Now some scientists such as Norman Letvin of Harvard think that HIV vaccine is not possible at all and instead we should think about stopping disease progression.

Not everyone thinks like Letvin though and after the failure of Merck vaccine scientists have started thinking about alternative ways of generating HIV vaccines. Evolutionary biologists have long known about endogenous retroviruses,the viruses that were once infectious but millions of years ago they somehow got incorporated in our genome and toady they exist in dysfunctional state in the genome. One idea is to figure out a way to endogenize HIV like its ancient relatives.

In addition, the Nixon group reported in the journal Plos Pathogens that immune response against the endogenous retrovirus may help in getting rid of HIV infected cells. One way that can happen is by killer cells killing HIV infected cells expressing endogenous retroviral protein on the surface. Another way is more direct: sometimes endogenous proteins are so similar to HIV proteins that the killer cells that recognize these endogenous proteins can also recognize HIV infected cells and kill them. Whoa! Don’t get too excited yet because not many scientists think this will be enough to get rid of HIV from an infected person. Even if turns out to be enough, a lot more work still needs to be done in this area for any commercial product to come out in the market.

There is still hope though. Steve Deeks at UCSF has found patients called “Non-Term Non Progressors” that incredibly control HIV and immunodeficiency for a very long time without any medications. Only about 5-15% of HIV infected patients fall in this category. Even remarkable are those people known as “elite controllers” that can control the virus for over 25 years without any medications. Deeks is studying these patients and trying to decipher what causes them to be so successful in the battle against HIV.

Scientists have insinuated various factors that may play a role in viral control. While some immune cells have been thought to play a role in this immunity, host genetics has also been shown to play a part in controlling HIV. For example, HLA B57 (B5701 in Caucasians and B5703 in Africans) and HLA-B27 alleles may play a role in HIV. Furthermore, in addition to the CCR5 delta 32 mutation other CCR5 mutations along with CCL3L1 gene polymorphisms may play a role in HIV resistance and/or control.

Therefore, a holistic look at all components, both immunological and genetic factors need to be considered while thinking about HIV vaccines. We are entering the era of personalized medicines and gene therapy. May be we will find one or a combination of genes that can protect us from HIV.

Images: Worldwide data on HIV infected people by countries (obtained from Merson et al, the Lancet, vol 372, Aug 09, 2008) Click on the images to download the original size.




Filed under Evolution, HIV, My Life My Thoughts