Gene duplication and molecular promiscuity
Peregrinations of a restless soul
I am at the end of Walter Isaacson's excellent biography of Steve Jobs and it's worth a read even if you think you know a lot about the man. Love him or hate him, it's hard to deny that Jobs was one of those who disturbed our universe in the last few decades. You can accuse him of a lot of things, but not of being a lackluster innovator or product designer.
Last week's issue of Nature had a special section on autism research. One look at the series of articles should convince anyone how complex the determination of causal factors for this disorder is. From a time when pseudoscientific environmental factors (such as "frigid" mothers) were supposed to play a major role, we have reached a stage where massive amounts of genetic data are uncovering tantalizing hints behind Autism Spectrum Disorders (the title itself pointing to the difficulty of diagnosis and description) without a clear indication of causes. Indeed, as pointed out in the Nature articles, some researchers think that the pendulum has now swung to the other side and environmental factors need to be taken into account again.
A ditty often attributed to Paul Dirac conveys the following warning about doing scientific work in your later years:
This year's Nobel Prize for physics was awarded to Saul Perlmutter, Brian Schmidt and Adam Riess for their discovery of an accelerating universe, a finding leading to the startling postulate that 75% of our universe contains a hitherto unknown entity called dark energy. All three were considered favorite candidates for a long time so this is not surprising at all. The prize also underscores the continuing importance of cosmology since it had been awarded in 2o06 to George Smoot and John Mather, again for confirming the Big Bang and the universe's expansion.
In the tradition of physicists writing for the layman, Robert Laughlin has emerged as a writer who pens unusually insightful and thought-provoking books. In his "A Different Universe" he explored the consequences and limitations of reductionism-based physics for our world. In this book he takes an equally fresh look at the future of energy. The book is not meant to be a comprehensive survey of existing and upcoming technologies; instead it's more like an assortment of appetizers designed to stimulate our thinking. For those who want to know more, it offers an impressive bibliography and list of calculations which is almost as long as the book itself.
For me, the most astounding thing about science has always been the almost unimaginably far-reaching and profound influence that the most trite truths about the universe can have on our existence. We may think that we are in charge of our lives through our seemingly sure control of things like food, water, energy and material substances and we pride the ability of our species to stave off the worst ravages of the natural environment such as disease, starvation and environmental catastrophe. We have done such a good job of sequestering ourselves from the raw power of nature that it's all too easy to take our apparent triumph over the elements for granted. But the truth is that we are all without exception critically and pitifully beholden to a few numbers and a few laws of physics.
With his colorful personality and constant propensity to get into all kinds of adventures, Richard Feynman is probably the perfect scientific character to commit to comic book form, so in one way this graphic novel is long due. What is remarkable is how powerfully Jim Ottaviani and Leland Myrick harness this unique medium to accurately dramatize the life and qualities of this genius. Both authors are uniquely qualified for this endeavor, having already penned graphic portraits of Niels Bohr, Robert Oppenheimer and Leo Szilard.
So it's that time of the year again, the time when just like Richard Feynman and Paul Dirac, three lucky people get to mull over whether they will incur more publicity by accepting the Nobel Prize or rejecting it.
Labels: Nobel Prize
In this year’s Lindau meeting, the Israeli biochemist Ciechanover expressed great hope for the future of personalised medicine, an age in which medical treatments are customized and tailored to individual patients based on their specific kind disease.
In some ways personalised medicine is already here. Over centuries of medical progress, astute doctors have fully recognized the diversity of patients who are suffering from what appears to be the same disease. Based on their rudimentary knowledge of disease processes, empirical data and experience, physicians would then prescribe different combinations of medicines for different patients. But in the absence of detailed knowledge of disease at the genetic and molecular level, this kind of approach was naturally subjective; it continued to rely on extensive personal experience and ad hoc interpretations of incompletely documented empirical data.
This approach saw a paradigm shift in the latter half of the twentieth century as our knowledge of DNA and genetics revealed to us the rich diversity and uniqueness of individual genomes. Concomitantly, our knowledge of the molecular basis of disease led us to recognize molecular determinants unique to every individual. We are already taking advantage of this knowledge and harnessing it to personalize therapy.
Take the case of the anticancer drug temozolomide for instance. Temozolomide is prescribed for patients with a particularly pernicious form of brain cancer with poor prognosis. The drug belongs to a category of compounds called alkylating agents, a common class of anticancer drugs in which a reactive chemical group is transferred onto DNA in cancer cells, rendering them incapable of efficient cell division and causing their death. The problem is that because of its key role in sustaining life processes, DNA division is tightly controlled. Any kind of modification of the kind caused by temozolomide is treated as DNA damage and- for good reason- life has evolved multiple mechanisms to reverse such damage. In this case the body produces an enzyme that strips DNA of the reactive functionality attached by the drug. Thus the body unwillingly helps cancer cells by reversing the drug’s action. The understanding of this mechanism has led doctors to personalize temozolomide treatment only for individuals who have low levels of the drug-resisting enzyme. For other patients that produce high levels of the enzyme, temozolomide will unfortunately not be effective and doctors will have to turn to other drugs.
We will undoubtedly witness the proliferation of such advances in personalizing individual treatments in the future. But what appears to be an even more promising approach is to start at the source, at the fundamental genomic sequences that dictate the phenotypical changes associated with enzymes and proteins. The deciphering of the human genome has opened up exciting and promising new avenues for mapping differences in individual genomes and harnessing these differences in drug discovery. The most important strategy has been to compare genomes of individuals for single nucleotide polymorphisms (SNPs) which are changes in single base pairs in the DNA sequence. In fact much of the genetic variation between individuals and populations arises from these single nucleotide changes. SNPs have been of enormous value in tracing genetic diseases and generally categorizing variations in our species. They are typically utilised in genome-wide association studies in which the genomes of members of a certain homogeneous population with and without a disease are compared. Knowing the differences can enable scientists to pinpoint genetic markers responsible for the disease. These genetic markers can then be linked to phenotypes like enzyme overproduction or deficiency that are more directly related to the disease. In addition SNPs are unusually stable and remain constant between generations, providing scientists with a relatively time-invariant handle to study genetic disorders. One of the most notable instances of using SNPs to determine propensity toward disease involves the so-called ApoE gene in Alzheimer’s disease. Two SNPs in this gene lead to three alleles- E2, E3 and E4. Each individual inherits one maternal and one paternal copy of the ApoE gene and there is now solid evidence that the inheritance of the E4 allele leads to a greatly increased risk of Alzheimer’s disease.
In the long run, SNP’s may provide the foundation for much of personalised medicine. This is because SNPs also often dictate individuals’ propensity toward drugs, pathogens and vaccines. Thus in an ideal scenario, one might be able to predict a patient’s response to a whole battery of drugs using knowledge of specific SNPs associated with his or her disease.
Unfortunately this ideal scenario may be much farther than imagined. For one thing, we have still only scraped the surface of all possible SNPs, and there are already an estimated three million out there. But more importantly, the difference between knowing all the SNPs and knowing their causal connections to various diseases is almost like the difference between a list of all human beings on the planet on one hand and everything about their lives on the other; their professions, origins, hobbies, political views, family lives. Knowing the former is far from understanding the latter.
In this sense the problem with SNPs illustrates the problems with all of personalised medicine. In fact it’s a problem that plagues scientific research in general, and that’s the dilemma of separating correlation from causation. The problem is even more acute in a complex biological system like a human being where the ratio of extraneous unrelated correlations to genuinely causative factors is especially high. Simply knowing the SNP variations between a healthy and diseased individual is very different from being able to pinpoint the SNP that is directly connected to the disease. The situation is made exponentially more complex by the fact that these putative determinants usually act in combination with each other. Thus one has to now account not only for the effect of an individual SNP but also for the differential effects of its combination with other SNPs. And as if this complexity were not enough, there’s also the fact that many SNPs occur in non-coding regions of the human genome, leading to even bigger questions about their exact relevance. Sophisticated computers and statistical methods are enabling us to sort through this jungle of data, but as of now the data itself clearly outnumbers our ability to intelligently analyse it. We need to become far more capable at distinguishing signal from noise if we are to translate genetic understanding into practical therapeutic strategies.
In addition, while a certain kind of SNP may be able to determine disease tendency, there are also many false positives and negatives. Only a small percentage of SNPs are typically linked to a condition, especially when it comes to complex conditions like cancer, diabetes and psychological disorders. Many SNPs may simply be surrogate SNPs that have little to do with the disease themselves but which have come along for the ride with other SNPs. It is a difficult task to say the least to separate the wheat from the chaff and hone in on the few SNPs that are truly serving as disease determinants or markers. In such cases it is instructive to borrow from the example of temozolomide and remember that ultimately we will be able to untangle cause and effect only by looking at the molecular level interaction of drugs and biomolecules. No amount of data sequencing and analysis can really be a substitute for a robust study designed to directly demonstrate the role of a particular enzyme or protein in the etiology of a disease. It’s also worth noting that such studies have always benefited from the tools of classical biochemistry and pharmacology, and thus practitioners of these arts will continue to stand on an equal footing with the new genomics experts and computational biologists in unraveling the implications of genetic differences.
Finally, there’s the all-pervasive question of nature versus nurture. Along with genomics, one of the most important advances of the last decade has been the development of epigenetics. Epigenetics refers to changes in the genome that are induced by the environment and not hard-coded in the DNA sequence. An example includes the environmentally stimulated silencing or activation of genes by certain classes of enzymes. Epigenetic factors are now known to be responsible for a variety of processes in diseases and health. Some of these factors can even operate in the fetal stage and influence physiological responses in later life. While epigenetics has revealed a fascinating new layer of biological control and has much to teach us, it also adds another layer of complexity to the determination of individual responses to therapy. We have a long way to go before we can perfect the capability to clearly distinguish genetic from epigenetic factors as signposts for individualized therapy.
The future of personalised medicine is therefore both highly exciting as well as extremely challenging. There is much promise to be had in mapping the subtle genetic differences that make us react differently to diseases and their cures, but we will also have to be exceedingly careful in not leading ourselves astray with incomplete data, absence of causation and confirmation bias. It is a tough, but ultimately rewarding problem which will lead to both fundamental understanding and new medical advances. It deserves our attention in every way.
I have stayed away from the Anna Hazare story mostly because I have had mixed feelings about it and because it's not really been high on my list of interesting topics. However I have to say that I am bamboozled by those who call Hazare's fast-unto-death "undemocratic" and say that he is "blackmailing" the government. Blackmail is when you force someone to do something against their will and threaten to harm them if they don't accede. Hazare is threatening to harm himself, so I don't see how it is blackmail. Now sure, people can call it blackmail because he is indirectly trying to harm the government by encouraging people to come out on the street in throngs. But how can he be held responsible for what the people do and do not decide to do based on his protests?
Labels: indian politics
Recently I read a comment by a leading chemist in which he said that in chemistry, intuition is much more important than in physics. This is a curious comment since intuition is one of those things which is hard to define but which most people who play the game appreciate when they see it. It is undoubtedly important in any scientific discipline and certainly so in physics; Einstein for instance was regarded as the outstanding intuitionist of his age, a man whose grasp of physical reality unaided by mathematical analysis was unmatched. Yet I agree that "chemical intuition" is a phrase which you hear much more than "physical intuition". When it comes to intuition, chemists seem to be more in the league of traders, geopolitical experts and psychologists than physicists.