On the Selfish Gene

I finally got to finish Richard Dawkin’s The Selfish Gene, 30th Anniversary Edition (it was originally published in 1976) and it tells a wonderful story of evolution by focusing on the gene. Dawkins revamps my understanding of biology by proposing a gene-centric view of life. He then introduces the notion of “replicators” and “vehicles”. You can call the first self-reproducing molecules replicators, and you may also be tempted to designate the same label to living beings today. Not exactly, according to Dawkins. It is in fact the gene within living organisms that are replicators. What does that make us? We are in fact the vehicles created by a conglomerate of genes in order to propagate themselves. Dawkins himself marvels at this incredible notion:

We are survival machines – robot vehicles blindly programmed to preserve the selfish molecules known as genes. This is a truth which still fills me with astonishment.

This is an unsettling thought, but it is evidenced by nature where genes and organisms are in conflict – such as the mating behaviour of the male of some species of spiders. It also has interesting implications. Parasites that are able to transmit their genes using the same outlet as their host (e.g. through sperm and eggs) eventually fuse into their hosts and become part of the host organism. What was once a parasite becomes a symbiotic part of the host – and this could explain the evolution of eukaryotes – which conspicuously harbour mitochondria and chloroplasts of different DNA from the cell nucleus.

Our own body contains trillions of somatic cells which do not participate in producing gametes. But therein lies their role in helping the germ cells produce gametes, for without the support from somatic cells, the germ cells would perish. A tantalizing analogy given is the eusocial bee’s hive where the worker bees are sterile and only the queen produces offspring.

The “selfish” gene theory ironically explains other biological phenomena such as kin selection and altruism. Kin selection works because genes that encourage an organism to help relatives (which are likely to contain the same gene) will increase the likelihood of transmitting itself to the next generation. Since we are likely to be surrounded by kin, any gene that promotes altruism also becomes successful by the same token. Thus these “selfish” genes actually result in unselfish behaviour in organisms. Dawkins cites the Prisoner’s Dilemma, which is a well known problem in game theory, and shows us how a “nice guy” strategy, or tit for tat proves to be most advantageous in iterated games.

Let us understand what our own selfish genes are up to, because we may then at least have a chance to upset their designs, something that no other species has ever aspired to do.

There are some who may misconstrue that our “selfish” genes advocate for us to live selfishly. But this is hardly the case, as although our genes may be “selfish”, they have created wonderful vehicles that do behave with reciprocal altruism. Perhaps then, contrary to what we may think, the selfish gene has ultimately become the cooperative gene and nice guys do finish first.

Note: For an online interactive game of “Prisoner’s Dilemma” visit http://www.iterated-prisoners-dilemma.net/.

Combating Medical Ignorance One Comic Strip At A Time

I’ve been away because I just finished my (gruelling) paediatric posting exams – paediatricians are generally very nice people, the kids are adorable but somehow paediatric exams can be nasty and it can all go downhill before you know it.

Back on topic – despite the fact that patients today are more educated than ever before on their illnesses, medical ignorance has become a serious problem. Parents stop vaccinating their children on unfounded fears of autism. A woman with treatable, early stage breast cancer delays surgery to try out an herbal remedy that her friend had tried. It is peculiar that human beings are so rigid in thought that they “believe what they want to believe” in the face of overwhelming solid evidence. Anecdotal stories from trusted friends are sensationalized by the media, and this steers public opinion away from scientific proof. The effects of medical ignorance can be deadly. Measles and mumps are making a comeback wherever vaccination rates drop, and people who delay treatment of initially treatable diseases inevitably return when it is too late.

I found this incredible series of comic strips by British artist Darryl Cunningham to be most useful in clear public ignorance on scientifically unproven medical myths such as the MMR-Autism debacle. Recently it has been updated with a new comic strip on homeopathy and I have to say I’ve become a fan of his work.

It’s well worth reading the rest of Homeopathy at his website. I’d also like to point you to his first strip on the Vaccine-Autism myth called the Facts In The Case of Dr. Andrew Wakefield. If you’re interested in more, the author also has a graphic novel, Psychiatric Tales, which features his experience in an acute psychiatric ward, mental illness, and ultimately his own struggle with anxiety and depression while training as a psychiatric nurse. Here’s a sample:

Killer Art

There’s a new exhibition at the Heller Gallery in Manhattan called Infectious Beauty by acclaimed multidisciplinary artist Luke Jerram in collaboration with University of Bristol virologist Dr Andrew Davidson. Is it wrong that I find these glass sculptures (of some of the most deadly viruses and pathogens known to mankind) simply exquisite?

HIV

Smallpox virus

Escherichia coli

Swine Flu Virus

To acknowledge the rapid mutation of influenza viruses they have even created “Untitled Future Mutation”.

Untitled Future Mutation

To me, these sublime glass creations are both awe-inspiring and creepy. Perhaps this is the intention of the artist – to show that there is beauty in even the tiniest and most deadly microbes.

Why I’m An Agnostic

Today I was evangelized by a young paediatric oncologist who preached about how his belief in God helped him through medical school and work, keeping him away from the peer influences of alcohol and drugs. This incredibly nice but stoic doctor shared with me the New Testament and encouraged me to find a church.

Many people ask me where I stand on religion. Honestly, it’s not an easy or straightforward question to answer. I was brought up in a family who did not discuss God or religion, and even looked down on the overly religious. Nevertheless, my upbringing was no less conservative nor sheltered. From an early age I’ve always read about science and my fascination for it remains strong to this day.

The concept of religion really hit me in secondary school when I did not fit into any peer group. I was attracted to the Christian community because it seemed wholesome and understanding when most kids were nasty and mean. Hence, I decided to join a Christian fellowship, not once, but twice. It was easy to depend on a higher being for guidance and assistance. However, I’ve always felt on the outs when it came to worship. In the back of my mind, science rather than religion could answer the curiosities I had about the natural world. Religion seemed dogmatic and restrictive, especially here where the Evangelical Christians are influential with their brand of conservatism. Being oppressed for being different from my peers taught me to be tolerant, understanding and liberal.

But I was humbled by the kindness that some Christians showed me, and I accepted Christ via the Christian Fellowship in 2006. 4 years later, where do I stand? The Christian friends that I cherished so much have mostly faded away. It made me think to myself, was I just a tool, a “pawn” to be converted so that they could receive a blessing from their “King”? The Christians I met after that seemed dubious, hypocritical and shallow.

I never really appreciated the love and kindness that seemed to radiate from Christians until I saw how selfish and self-preserving those without religion can be. This highlights the stereotypical image problem of the solitary and un-altruistic atheist. The Church, for all its troubles and dogma, is a huge charity that helps out the community. Sure, there are many charities that are secular in nature, but are atheists too busy bashing religion to create a closely connected community? This brand of aggressive atheism is just as forceful as the evangelical movement and will meet strong opposition rather than understanding. (Disclaimer: I’m a huge fan of Richard Dawkins’ works on evolution, but even I can agree that his aggressive atheism is sometimes obnoxious)

To me, religion is probably a by-product of our ever-expanding brain capacity. It is the earliest “science”, where humans tried to explain the world at a time when they did not have the advanced tools to study natural phenomena. Evidently, spirituality has evolved separately in most cultures worldwide. Religion is the organization of this spirituality, with an authoritarian power.

Organized religion is something that I am against. I think it is healthy for people to develop their own unbiased thoughts and opinions and this is suppressed by organized religion. Science promotes critical thinking and at its best constantly forces us to challenge our own thoughts. It is this challenge, looking at things from different angles, self-reflecting on my own thought processes that made me highly curious on what makes people tick.

My opinion is that the concept of God is a perfectly natural part of the evolution of any sentient being that has acquired a reasonable amount of intelligence. Without religion, human history would be radically different. Religion has played a huge role in the rise and fall of civilizations around the world, and scientific progress could not be achieved without civilization. As science progresses by leaps and bounds, is religion truly still relevant? Perhaps, but not in its present shape or form. Human beings have this existential need that can be satisfied by spirituality. But it can also be satisfied by a thorough and competent understanding of science. Currently I straddle these two notions. Spiritually I feel connected to the concept of God, yet I do not feel obliged to follow religion dogmatically. I am also aware that it is through science that I can truly understand the natural world – and this gives me the greatest satisfaction.

Hence, I would classify my beliefs as agnostic in nature, which is the belief that the truth value of the existence of God cannot be known. Agnosticism plays an important role in the philosophy of religion because it poses a serious challenge to those theologians and philosophers who argue that knowledge about gods is possible. If agnosticism can be successfully defended as being at least rational, then the efforts of many religious apologists (especially those who try to prove the existence of God) can be called into serious question, if not rejected entirely as a castle built upon sand.

I do not believe in the literal interpretation of the Bible, but I do believe in the intrinsically good message that it has. Nevertheless, my liberal curiosities are entrenched in the scientific method rather than religion. I enjoy this unrestrained freedom of thought at the cost of feeling like an outsider in the conservative Christian community. Moreover, I do identify with the more secular minded community but this community is especially rare for there is a line between secularism and being just plain ignorant (most people I meet are unfortunately laodicean when it comes to religion and science). My hope is that atheists and agnostics can build a stronger community of mutual interests so that science can be promoted peacefully rather than forcefully. Although we are all made up of “selfish genes”, to act selfishly is shortsighted because I strongly believe our genes resulted in behaviour that is altruistic in nature.

Were Mesozoic Sea Monsters Warm-Blooded?

Warm-bloodedness is the ability of an animal to maintain their body temperature at a roughly constant level, regardless of the environmental temperature. However, this term has now fallen out of favour in lieu of more specific definitions of thermoregulation.

Endothermy is the ability to regulate body temperature via internal mechanisms that generate heat such as muscle shivering or fat burning. In other words,  the concept is similar to an internal “furnace”.

Homeothermy is the ability to maintain a constant internal body temperature that does not depend on the external temperature.

Tachymetabolism refers to the ability to control body temperature by having a high resting metabolism.

The reason why there are 3 definitions for warm-bloodedness is because scientists have discovered that not all traditionally warm-blooded animals (mammals and birds) fit into all categories. On the flipside, some “cold-blooded” animals such as the bluefin tuna and mackerel shark display some features of “warm-bloodedness”

In the Mesozoic era, while the dinosaurs conquered the land, 3 general groups of fascinating reptiles ruled the seas; the dolphin-like ichthyosaurs, the long-necked plesiosaurs and the serpentine mosasaurs. A study in the June 11th issue of Science suggests that these top-tier sea creatures could have displayed some features of warm-bloodedness. How did they arrive at this tantalizing conclusion?

Well, warm-bloodedness leaves clues even in the fossils of long dead animals. The ratio of various isotopes of oxygen are preserved in the phosphate minerals of tooth enamel. Isotope geochemist Christopher Lecuyer then compared the proportion of oxygen-18 isotope in the tooth enamels of  ichthyosaurs, plesiosaurs and mosasaurs to those of the presumably cold-blooded fish in the same geologic strata.

What they found was that the marine reptiles had a higher proportion of oxygen-18 compared to the cold-blooded fish. This suggests that they had some degree of warm-bloodedness. The researchers concluded that ichthyosaurs and plesiosaurs had body temperatures of about 35-39 degrees Celcius, which is a whopping 20 degrees warmer than the sea temperature. Like tuna and swordfish, which are homeothermic and endothermic, ichthyosaurs and plesiosaurs could have generated heat from the muscles in their body.

Elasmosaurus, a plesiosaur, and one of my favourite prehistoric creatures.

Tylosaurus, a mosasaur, chomps down on a meal in the Late Cretaceous.

A school of Shonisaurus, the largest ichthyosaur discovered, roam the late Triassic seas

The marine sea reptiles were a huge evolutionary success, dominating the mesozoic seas. Warm-bloodedness may have played a key role to the success of ichthyosaurs and plesiosaurs because studies of body plans have suggested that these creatures were pursuit predators that needed to stay active to hunt. The evidence for mosasaurs is more equivocal but still enough to conclude that they had some degree of temperature control. This could be explained by the idea that mosasaurs were ambush predators that required less energy. Nevertheless, this study gives us enticing proof of how warm-bloodedness evolved in these majestic aquatic reptiles from their cold-blooded land cousins

Copy Number Variations and Autism

Autism is a life-long neurodevelopmental disability that is characterized by a triad of symptoms;

(i) impairments in social interactions,

(ii) impairments in communication and

(iii) restricted interests and repetitive behaviour.

These symptoms appear before the age of three and it affects boys more than girls (4.3:1). The rapid rise of autism cases being reported over the last decade is as mystifying as the cause of autism itself (claims of a vaccine link have now been firmly debunked).

The impaired social interactions of autistic people stems from an inability to read social cues. Thus they may appear distant, preferring to be left alone or exhibiting social awkwardness in making and maintaining relationships with other people. These social deficits are present from an early age. In autistic toddlers, there is a lack of eye contact. In addition, they smile less and have difficulty with social gestures. Children with autism fail to develop peer relationships that are appropriate with their developmental level.

In autism, there is a delay or total lack of the development of spoken language. Moreover, in those that have adequate verbal ability, they have difficulty beginning or sustaining a conversation with other people. There may also find it hard to understand metaphors and figures of speech, as they tend to interpret language literally. As children, autistic people show a lack of imaginative or make-believe play that is present in their peers. They are less likely to ask for something or share their experiences and are more likely to repeat others’ words (echolalia) and reverse pronouns (referring to themselves as “he”, “she”, “you”)

Besides that, autistic individuals display a variety of repetitive or restrictive behaviour. Characteristic and apparently purposeless movements such as hand flapping, head rolling or body rocking are common. Individuals with autism also have a ritualistic behaviour where they perform daily activities the same way each time. They have difficulty tolerating changes in routines and/or the environment (such as moving furniture). Another diagnostic criterion is an intense preoccupation with a narrow and restricted area of interest, for example in maps, trains or dinosaurs. Often, the autistic individual accumulates a vast amount of information on this particular interest.

It has long been known that autism has a genetic component. But previous studies only accounted for a fraction of the genetic causes of autism. Recently, copy number variations were reported in Nature to be 20% more common in children with autism. What are copy number variations? We are perhaps most familiar with the idea that chromosomes come in pairs, and hence we have 2 copies of a any particular gene, neatly tucked in each chromosome. We are familiar with the idea that mutation happens when a base in the gene itself is not copied correctly, causing an error. However, since the human genome project was completed in 2006, researches have found that there is more to our genetic makeup.

Copy number variation

Let’s say there’s an imaginary chromosome A and it has a pair, chromosome B. On the long arm of both chromosomes A and B lies a copy of a gene, which we shall call K. Sometimes during cell reproduction, part of the long arm of chromosome A gets accidentally duplicated. The result is that chromosome A contains 2 copies of gene K , and adding this up with the copy of gene K on the matching chromosome B, we get a total of 3 copies. This is called copy number variation – quite simply it is the variability in the number of copies for a gene. To illustrate this point further, the amylase gene is present in European Americans in a range from 2-15 copies. The more copies of the amylase gene, the faster the person can break down starch. Copy number variations account for  each individual’s uniqueness and they are actually quite common in the human genome.

According to the Nature article, these copy number variations could be inherited from parents. Strikingly however, these events also happened de novo. This means the mutation are not found in the parents, but arose spontaneously in the child’s DNA. This can happen when errors occur in the formation of the parental gametes, which are then copied into the child’s DNA. The unique genetic disruptions found in the children studied increased their genetic susceptibility to autism. Hundreds of both inherited and de novo copy number variations have been found in the DNA of the autistic children studied. Hence, autism is better thought of as a group of diseases rather than a single entity – which poses more questions rather than answers.

How Endogenous Retroviruses Predict Evolution by Common Descent

I highly recommend the Facts of Evolution Series on Youtube. In this latest installment, the author talks about retroviruses. These are viruses that reverse transcribe RNA into DNA (which is the opposite of what  most organisms do). Examples of such retroviruses are the HTLV-1 virus which causes leukemia and the HIV virus which causes AIDS. However, some retroviruses can insert their DNA into host germ cells where they are inherited by descendants of the host. These are called endogenous retroviruses (ERV), and they persist in the genome of the species that becomes infected.

Under the idea of common descent, we can predict the evolutionary relationships of different species by comparing their genomes and identifying ERVs. If the ancestor of humans have acquired ERV1 after the split from other apes, we can expect to find ERV1 in the genome of all humans but not in the genome of any other ape. With the advance of genetics, scientists are comparing ERVs between species and so far everything has added up, thus providing another strong evidence for evolution.

Interestingly, where mammals except monotremes are concerned, ERVs are known for role in allowing pregnancy to occur. During pregnancy, some ERVs are turned on and they cause an immunosuppressive effect to protect the embryo from the maternal immune system. It is thought that at some point a retrovirus infected an early mammalian ancestor, and this enabled the evolution of vivaparity as the fetus became more resistant to the mother’s immune system. They also play a role in the formation of the placental syncytium, via viral fusion proteins. An example of a viral fusion protein in retroviruses we see today is gp41 seen in HIV.

Jupiter: Guardian or Menace?

The 5th “rock” from our sun is actually a huge ball of hydrogen and helium. 2.5 times larger than all the other planets in our solar system combined, it is no surprise that Jupiter has the largest gravitational pull of any other object besides the sun itself. Almost 1 year ago it was hit by a rogue 1600 ft asteroid that caused a blemish the size of the Pacific Ocean in it’s atmosphere that was even visible to backyard astronomers. And just a few days ago, in a major coincidence as images from last year’s collision are released, another space rock made its final collision with the gas giant, captured separately by two backyard stargazers from Broken Hill, Australia and Cebu, Philippines.

This close frequency between Jovian impacts is puzzling to scientists who thought such events were relatively rare. In fact, after the much publicized Shoemaker-Levy 9 collision of 1994, astronomers had thought that it would be 50 to 250 years before the next impact. It also brings to mind a pertinent question; What is the effect of Jupiter on asteroid collisions on our own terra firma? Traditionally, Jupiter has been viewed as a shield that protects Earth from asteroids and comets by pulling them towards its massive gravitational well. However, this view is changing with research by Horner and Jones of Open University. According to Hal Levison of Southwest Research Institute who studies the evolution of our solar system, Jupiter is both a guardian and a menace, depending on where the space rock comes from.

The asteroid belt that lies between the orbits of Mars and Jupiter exists because the latter’s gravitational pull prevented the formation of a protoplanet. Jupiter probably has a harmful effect to us if the object comes from the Kuiper belt (shown in green below), a massive band of small asteroid-like bodies which lies beyond Neptune. This is also where our dwarf planets such as Pluto, Haumea and Makemake reside. The gravitational effect of Jupiter probably increases our exposure to the comets and asteroids from this band.

But beyond the Kuiper belt lies an even bigger threat. This is the hypothesized cloud of comets that lies almost a light year beyond the solar system – the Oort Cloud. This far away from the sun, they are susceptible to the gravitational effects of passing stars, and when that happens a stray Oort Cloud object could be sent spiraling towards us. The effect of Jupiter is such that it has kept most of these objects out of the solar system in the first place. Moreover it can deflect these objects when they come too close to the solar system.

Therefore, it seems Jupiter has both a positive and negative effect on asteroid and comet impacts on Earth. Although it increases the likelihood of collisions from the Kuiper Belt, it protects us from the bigger threat of Oort Cloud objects that are difficult to track due to their great distance.

A Slew of New Ceratopsians

I just found out that the past week has been a busy busy week for ceratopsian discoveries. Ceratopsians are among the last wave of magnificent herbivorous dinosaur groups to emerge in the late Cretaceous.

This is Coahuilaceratops magnacuerna (Koh-WHE-lah-SARA-tops mag-NAH-KWER-na) which is the first horned dinosaur unearthed in Mexico. Its latin name means “great horned face from Coahuila”. The most unique feature of this species which lived 72 mya is that it had horns up to 4 feet long, which is longer than any other ceratopsian.

The 1 metre long Ajkaceratops kozmai is small in stature but it represents the first ceratopsian discovery in Europe. In the late Cretaceous, Europe was an isolated island landmass and this find is evidence of island dwarfism and the migration of ceratopsians from Asia. This ceratopsian is probably a protoceratopsid related to Magnirostris.

Sinoceratops zhuchengensis is another important discovery because before this ceratopsids have been exclusively found in North America. This late Cretaceous dinosaur also blurs the distinction between 2 subfamilies of ceratopsids, the chasmosaurines and the centrosaurines.

This fearsome looking creature from southern Utah is appropriately named Diabloceratops eatoni (Latin for devil horned face). At 80 million years old, it is also one of the oldest ceratopsids. Has to be one of the coolest frill horns in the dinosauria.

Last but not least is this stunning specimen from the Montana-Alberta border. Christened Medusaceratops lokii for its curved, snakelike frill-horns which resembled the head of Medusa, as well as its arching brow horns which are reminiscent of the Norse God Loki, this beast lived 78 million years ago and grew up to 20 feet long.

The Cell Which Was Made By A Computer

You’re looking at 2 colonies of a bacteria called Mycoplasma mycoides. The center of the colony is blue because this bacteria contains a gene for an enzyme called beta-galactosidase. When a special substrate is added to the medium, beta-galactosidase will convert it into an insoluble blue dye. But these are no ordinary organisms. Genetic sequencing will reveal that its genome is unlike any other living bacteria of its kind. If you cracked it genetic code, you may find the names of 46 scientists as well as 3 poignant quotes:

“To live, to err, to fall, to triumph, to recreate life out of life,” from James Joyce’s A Portrait of the Artist as a Young Man

“See things not as they are but as they might be,”  from American Prometheus

“What I cannot build I cannot understand.” by Richard Feynman

This is because the genome of this unusual colony of bacteria has in fact been synthetically created by the computers of leading scientist Craig Venter (whom you may have been familiar with if you’ve read about the Human Genome Project). Using a computer to specify the genes, artificial DNA was synthesized in a sequencing machine. This DNA was then transported into the hollow corpse of a related bacterium, Mycoplasma capricolum. Then, scientists watched as the DNA expressed itself in the empty shell of the host. Physiological processes booted up, and the synthetic cell came alive ala Frankenstein. Not only is the artificially created bacteria functioning, it can also replicate to form the colonies seen above.

What are the implications of this landmark experiment? Contrary to public fears, this synthetic bacterium has had its genes for virulence deleted, meaning it is highly unlikely to cause disease. Other bacteria may soon be synthetically created in order to serve humans. Bacteria with the ability to produce biofuels such as hydrogen or absorb greenhouse gases such as carbon dioxide could become a reality.