Religion, science, and believing.

I don’t usually talk about my personal views on this blog. However, this topic is something that I have contemplated for a while now and think is fair to be open about. I am still learning and evaluating my outlook on approaching this subject. Below are some bits revolving around the themes of religion and personal belief systems that were hidden away in my drafts folder for a long time. I have decided to publish all of them together. I’m sure I’ll have more to say about this topic in the future, but here’s a start.

***

Recently, I had a conversation with a fellow grad student about religion and his personal beliefs. Most academics shy away from this discussion in a professional (and sometimes even in a personal) setting. It is considered uncommon or rude to talk about it and people keep it to themselves. It is often acknowledged that as scientists, “we do science for science’s sake”, or that “a person’s religious beliefs has no place in his/her scientific pursuits.” This is something that has always boggled my mind. As a biologist and an atheist, I have confidence in my work/study because the underlying laws of biological systems are established and follow a set of proven scientific principles. For example, when we design an antibacterial drug against a particular strain of resistent bacteria, we know for a fact that the bacteria has mutated (or evolved) and therefore the old drug doesn’t work anymore. Similarly, we use mouse, worm, and other animal models for testing compounds in vivo because we have evidence to prove that humans are genetically related to other animals through a common evolutionary ancestor. Therefore, we can study the effects of the drugs in other animals before testing them to humans. The empirical evidence that exists as the basis of our research is inherently acknowledged to be the underlying force that drives scientific research. Now, how can someone who does similar work in a laboratory setting have a completely contradictory viewpoint in his/her private life? How can someone believe in a book (or many books) that preaches blatant falsehoods about our understanding of the universe and at the same time come to work every day and do science with a conscious mind? For me, science is deeply woven into our personal lives. No, I cannot pretend that science does not affect my personal views about the world. Similarly, my conscious will never let me pretend like my personal views have no affect on my scientific work.

***

One of the most common arguments that I have come across during such discussion is that people often say “I don’t believe in *everything* that this book says. I only believe in a few things that are important for my moral framework.” This is complete BS and hypocritical. One cannot disregard a particular theory written in a book (for example, “the earth is 6000 years old”, or, “when humans die we come back as another life form on earth”), and at the same time believe in another theory written in the same book. One can’t pick and choose what you want to accept and reject from a book, and then claim the book to guide one’s moral framework.

And then there is an argument that science is not perfect and that not everything published in all of the scientific literature is true. This is absolutely correct. This is why science is constantly changing – because our understanding of the world is constantly changing. This is why scientific literature constantly undergoes modifications and updates to accommodate our latest understanding of the world and the universe.

This is not the same with religious texts. These texts were written hundreds and thousands of years ago and are obsolete in this day and age. These texts were written to accommodate the worldview of an ancient time period. They are not relevant to the 21st century and we certainly do not have to submit to these texts in order to live within a moral framework of society. As of 2017, we have discovered around 8.7 million species on earth and can estimate a hundred billion galaxies in the observable universe. We have achieved things that were once considered unfathomable by humankind. Why do we have to be stuck in the ancient past and live by some 12th century law in order to be considered as “good humans”? Of course, religious texts provide interesting insight into various philosophical questions that one can ponder over. However, they do very little to the understanding and practice of science in this day and age.

It is also often argued that we need religion to understand morality and differentiate between good and evil. Religion does not equal morality. One does not have to be a good human just to please an invisible supreme being or to go to heaven. Altruism and kindness can exist on their own.

***

Talking about scientists with personal religious beliefs, I remember a wonderful conversation between Richard Dawkins and Lawrence Krauss many years ago. I can’t help but bring up a part of their conversation while thinking about this topic –

Krauss: I’ve had people write to me and say “I’m a medical doctor and I don’t believe in evolution.”

Dawkins: That’s a disgrace. I’m not supposed to say that, especially in this country (referring to the US) because one’s private beliefs are supposed to be irrelevant. But I would walk out of a doctor’s office and not consult him anymore if I heard that he said that. Because what that doctor is saying is that he’s a scientific ignoramus and a fool.

Krauss: In fact, in that regard, it is interesting to me at the same time how people can hold beliefs which are incompatible with other beliefs they have. And in some sense, everyone is a scientist and they just don’t realize they are, and yet in the time of crisis, that’s when.. (breaks). The example I gave is when George Bush was president, he said intelligent design must be taught alongside evolution so the kids will know what the debate is all about. And it wasn’t a stupid statement at priori, it was ignorant because he didn’t realize that there’s no debate. And that’s fine. I don’t mean ignorant in a pejorative sense, I just mean he wasn’t aware.

Dawkins: Ignorance is no crime.. you just don’t want to consult a doctor who’s ignorant.

Krauss: What amazed me is that in the same administration, when the avian flu was going to be a problem and mutating to humans, president Bush said “We’ve got to find how long it takes before the avian flu will mutate into humans.” And what amazed me is that no one in the administration – not a single person said “It’s been designed to kill us, forget about it.”

Dawkins: That’s a very good point. This kind of split-brain business which you’ve been referring to, the most glaring example I know, is more in your field (referring to Theoretical Physics and Astrophysics) than mine. I was told by a professor of Astronomy at Oxford, about a colleague of his who’s an astronomer and an astrophysicist, who writes learned papers – mathematical papers, published in astronomical journals, assuming that the universe is 13.7 billion years old. But he privately believes that the universe is only 6000 years old. How can a man like that hold down a job in a university as an astrophysicist? And yet, we are told “Well, it’s his private beliefs, you mustn’t interfere with this man’s private beliefs as long as he writes competent papers in astronomical journals”.

Krauss: Well, I mean, as long as he doesn’t teach his private beliefs.

Dawkins: Well, let’s hypothetically suppose that he teaches absolutely correctly – that the universe is 13.7 billion years old. How could you want to take a class from a man who teaches one thing and believes in something that is so many orders of magnitude different?

***

About believing in science.

My advisor once pointed out not to use the word ‘believe’ when someone said “I believe that..” during a lab meeting presentation. Back then, I didn’t understand what was wrong in saying we “believed” in something. I now understand. As scientists, we evaluate something on the basis of observation, experiment, and evidence. The evidence is dependent on the observations made and experiments performed. Therefore, something is either likely or unlikely to occur. It is either more probable or less probable. We don’t have to believe in evolution or the big bang theory. We accept the evidence that supports them. Believing in evolution or not doesn’t make it true. The evidence for evolution suggests that it is true. Belief is not a part of rational enquiry. Belief relies on faith and not on evidence.

Advertisements

[Almost] one year milestone – my first advisory committee meeting

Advisory committee meetings are held once every year (or twice every year, if the student or the committee chooses to do so) to asses the progress of a grad student’s PhD thesis. The meeting involves a written report that is to be submitted to the committee a week prior to the meeting and an oral presentation on the D-Day. During the presentation, the validity of the research work is thoroughly discussed along with the future direction(s) of the project(s) being undertaken. The advisory committee meetings are extremely important for the successful advancement and completion of a thesis – it is where brutal yet honest feedback is conveyed. We as grad students are forced to think critically of our work and defend our hypotheses as well as our results.

My first advisory committee meeting was an intense two-hour long session on a rather dull Tuesday afternoon. As I explained the premise of my work and my goals for the next year, my committee members brought up important questions that I had not previously ever considered. All the members of my committee, including my advisor, were supportive and encouraging. I learned some valuable lessons from the entire experience and got some great feedback from everyone. Some interesting and important points highlighted in my feedback assessment were –

  • Think carefully about how to present data and set up an argument in my presentation.
  • Work on clearly identifying the premise that sets the stage for my hypotheses.
  • Be critical about my data.
  • Continue to read literature: more reading, and reading more critically.
  • Focus on developing more robust immunological assays to answer the questions in my aims.
  • Interact more with colleagues on campus and at other schools to learn and get insight into techniques and relevant assays (wrt understanding what works and what doesn’t).
  • Explaining the experiments in detail before delving into my results (every assay is unique and has a question to be answered).
  • Think about how I want to present the previous studies done in the field that are relevant to my questions.
  • My hypotheses should be provided with a context (what is the data in support or against my hypotheses?)

These were just some of the significant parts of the feedback that I received. Now it’s time to put these into action and definitely work on continuing to build on my project more confidently. More later.

Thoughts on lab rotations

The thing with first-year rotations in a Ph.D. program is that anxiety starts kicking in somewhere along the way when you consciously identify the lab that you want to join and want to get started right away. Having realized that this is going to be a long journey and rushing into things may not help, I am now gaining patience and perspective, and hope to make the most of the remaining time of my first year.

Rotations are a great way to learn about a lab and get involved in the nitty-gritty of research. I was warned at the beginning by a few seniors that I would either love a lab or reject it within the first few weeks of the rotation. Mind you – this has nothing to do with the science pursued in the lab (one wouldn’t decide to rotate in a lab if they didn’t find the research interesting in the first place). This is more about getting comfortable with the way a lab functions and deciding if the environment is a good fit for you. An eight-week lab rotation is really like an eight-week long interview with a potential PI and the lab! It is essential to identify the kind of relationship you foresee having with your advisor for the next couple of years (and beyond). This is perhaps one of the most important aspects of a rotation for me, next to the research work. A good mentor-mentee relationship can go a long way and can be extremely beneficial to one’s academic/professional career. I prefer having an open channel of communication with my mentor and learn as much as possible from him/her.

Not all graduate programs require laboratory rotations. Many departments or programs accept or reject students simply based on their application and/or an interview. In the UK for example, students are recruited to work on specific projects and grants as a part of their Ph.D. for the time period of around 3 years. This may not benefit the candidates who wish to propose their own ideas and develop their own thesis based on their individual research interests. In the US, for most graduate programs in the life sciences (mainly biology and chemistry), the average time for graduation is around 5-6 years. I believe that the freedom and independence of this system trump the short graduation time of the other systems. Although I am certain that both sides have their set of merits and demerits, at the end of the day, the journey is unique to each one of us and what we make of the experience matters the most.

Blots, cultures and assays concludes rotation two

This week officially concludes my second laboratory rotation in the neuropharmacology lab with research focussed on  G protein-coupled receptors and their application in several neurological disorders such as depression and anxiety. In the eight week duration of my rotation, a few things were achieved with respect to validating the activity of the newly developed M4R-DREADD (a designer M4 muscarinic receptor exclusively activated by a designer drug). Designer receptors are engineered such that they are solely activated by a synthetic ligand. This opens new avenues in the activation and control of G protein-coupled receptors’ function in vivo.

After a long break from my Master’s research, I got back to maintaining two cell lines – CHO (Chinese Hamster Ovary) and HEK293 (Human Embryonic Kidney) cells, in which the opioid receptors were expressed for all my experiments. These cells were used to characterize the receptor signaling by western blot analysis of the downstream MAPK/ERK signaling  upon stimulation by a few agonists/drugs of interest. Luckily, the lab acquired a new fluorescence microscope during this period which helped us observe the recruitment of the β-arretin2 protein by δ-opioid receptors in HEK293 cells stimulated with clozapine-n-oxide, a synthetic ligand.

mrrd-gfp barrest-cherr cno 0 min 20x_Overlay copy
HEK293 with M4R-dreadd 20x
mrrd-gfp barrest-cherr cno 10 min 20x_Overlay copy
HEK293 with M4R-dreadd 20x

This week, I had a lot of difficulty in handling the mice. Being my first experience with animal work, watching the mice anxious and struggle while we held them down was hard. I am still pretty unsure about how I feel about animal work (if I HAVE to do it to save my research in the future, I will) but I definitely need more exposure and practice with them.

Overall, this lab taught me a lot, even if some days were stressful and  tiring. I feel like I learned and enhanced many skills in the process (primer design, restriction analysis, cell culture, cloning, western blot, cAMP assay), and got a feel for the lab at the same time. Through the course of these past two rotations, I have met some really smart and dedicated people. In the end, I am grateful to have had this opportunity.

Orientation week: What do I want out of grad school?

The first week of grad school was intense and exhaustive with all kinds of information being tossed at us from all directions. We started off with a formal introduction to the school, the department, and all the resources available at our disposal like the libraries, mentors, health benefits, and so on. Besides all this, a main objective of the orientation week was to decide the first two labs that we are interested to rotate in. The process involved meeting with several professors, going on lab tours, meeting other grad students and evaluating if a lab was a good fit for us or not. Although I knew the direction of research I wanted to pursue, discovering so many options and learning about cool new research areas left me wondering if I really knew what I wanted to be doing for the next five years! Right now, I feel like a first grader starting school for the first time and constantly being exposed to many things I never knew existed.

Grad school 101 - What I don't know
Grad school 101 – What I don’t know

Being in a big umbrella program, there are ten different training groups to choose from. First year graduate students pick four labs within any of the groups to rotate in during their first year. This is very different from a departmental graduate program where a student can only rotate in labs within that respective department. After all the decisions and evaluations, I have chosen my first two labs for the semester and I am looking forward to be officially starting next week.

This process has made me question some decisions that I’ve taken in the last couple of years. “What do I want out of grad school?” seems to be the most significant one. Before beginning my journey, I knew that I wanted to train to be a good scientist, learn how to think, develop skills unique to my field, master techniques that will make me employable, learn how to learn, and be an overall well rounded researcher. Now I’m not sure if there is a definite answer to the question. It is something that I’d have to figure out on-the-go.

The Biology of Vaccination

I was never too involved in the vaccination debate until I came to the United States. Back home in India, the majority of us seem to be grateful to science for being able to wipe out dreadful diseases like MMR (mumps-measles-rubella) and polio, and prevent the lifelong suffering of thousands of people. A friend recently mentioned that his mother refused to vaccinate him as a child when she observed escalated fever-like-symptoms every time he got an immunization shot. This is one small example of a widespread scientific ignorance that lures people into believing in absurd anti-vax propaganda.

Let’s talk about the biology of vaccination. A vaccine is a weakened form of a disease-causing agent that boosts the immune system and provides protection against natural infection. This “agent” may be an altered form of the infection or its less dangerous close relative. A vaccine is usually combined with an adjuvant – a chemical that enhances the immune response. Prior to vaccination, a process known as variolation remained popular in the 17th and 18th century. In this, scab material taken from a mild form of smallpox was inoculated through the skin to curb the disease. Variolation was in no way harmless and therefore ceased to be in use when safer alternatives were sought. The history of vaccination is one of the most interesting stories in the field of science and medicine. Edward Jenner (the father of Immunology) – after having observed that milkmaids exposed to cowpox were protected from smallpox disease,  treated the locals with cowpox scabs and successfully prevented the occurrence of smallpox.

So how does vaccination work? I have briefly talked about the two main kinds of immune responses in one of my earlier posts. Further, acquired immunity consists of antibody (humoral) response and cell-mediated response that involves various types of white blood cells (WBCs) like macrophages, dendritic cells, T-lymphocytes and B-lymphocytes. When an infectious agent enters the body, chemicals called chemokines and cytokines recruit WBCs to the area of infection. The pathogen is broken down into its constituent proteins by Antigen-Presenting Cells (APCs) and is then “presented” to the helper T-lymphocytes (CD4+ T cells). These lymphocytes actively mediate protective immunity.

In humoral immunity, the receptors on B-cells recognize specific antigenic proteins, get activated and multiply to make hundreds of identical cells. Upon maturation, these plasma cells release a large number of antibodies that are specific to the antigen. This rapid increase in the number of antibodies is sufficient to eliminate the pathogen. Apart from the B-cells, cytotoxic T-cells (CD8+ T cells) also induce an immune response by directly destroying antigens that are presented by the APCs.

Primary exposure to pathogen via vaccine and secondary exposure to pathogen via infection - Sequence of events.
Primary exposure to pathogen via vaccine and secondary exposure to pathogen via infection – Sequence of events with respect to humoral immunity. Cell-mediated immunity works similarly through cytotoxic T cells – Activated cytotoxic T cells directly destroys the antigen. (Not shown) — CLICK TO ENLARGE —

When the infection is cleared, the immune response reduces and so does the number of antibodies and cytotoxic T-cells. During this time, some of the T- and B-cells become memory cells and preserve their antigen-specific surface receptor. These cells stick around in our serum and wait for a subsequent attack by the same pathogen. This is the crux of vaccination.

When our body is invaded by the same pathogen again, these memory cells immediately proliferate and release surplus of specific antibodies against it. This secondary response is faster and involves a greater number of cells, and is therefore more effective than the primary response. Vaccination establishes a pool of memory cells that are specific to the antigen and prepares the body in case of future infection. Therefore, when a weakened form of the pathogen is intentionally administered to us, our body develops an “actively acquired immunity” for a quicker and a more efficient secondary response.

Antibody response during primary and secondary exposure
Antibody response during primary and secondary exposure

The milkmaids from Edward Jenner’s anecdote had acquired an active immunity for smallpox virus because they were previously infected by the cowpox virus (both poxviruses, members of the Poxviridae family) due to their occupation. Also, when my friends mother observed an escalated fever-like symptoms after the vaccine shot, it was merely the body’s primary immune response to the infection – completely normal and a sign of an actively functioning immune system.

Though the science of vaccination is pretty forthright, many concern arises regarding its safety, constituents, production and side-effects. It is important to understand that every immune system is unique due to which every person may respond differently to different vaccines. Many of the health and safety claims (with respect to autism, mercury, formaldehyde, and so on) have already been debunked extensively by reputed scientific sources. Also, parents choosing not to vaccinate their kids against the government’s decision are endangering the rest of the community. Herd immunity works when the larger part of the population is resistant to a pathogen providing protection to those without immunity thereby preventing an outbreak. And finally, if you’re against vaccination due to your religious beliefs, please pack up and leave.

Interestingness –

  1. How the anti-vaccine movement is endangering lives
  2. The dangerous consequences of anti-vaccine propaganda in one map
  3. Understanding Herd Immunity
  4. 9 vaccination myths busted. With science!

Current issues with Genetically Modified crops

Humans have been modifying plants for thousands of years. Selective breeding or artificial selection techniques to improve plant quality have evolved into powerful tools for producing a large variety of plants. The biotechnology industry has developed newer techniques of genetic modification over the last twenty years. Genetically modified plants with specific traits can be created with great accuracy in a short amount of time compared to the conventional plant breeding methods that can often be inaccurate and time consuming. The European Commission in 2001 defined genetically modified organisms (GMOs) as “organisms in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination1.”

Credit: Courtesy of Wikimedia Commons
Credit: Courtesy of Wikimedia Commons

How are GM crops produced?

Genetic modification involves the introduction of a “gene of interest,” also called the “trans-gene” from another organism, usually bacteria, into the target plant in which a new trait is desired. These new traits could be: extending the life of the plant, making the plant resistant to pest attacks, tolerance to chemicals, slowing down natural decay, improving nutrient content, etcetera. Promoter and terminator genes that can switch on and off the gene of interest are introduced into the plant through the vector, along with a marker gene that signals the modification or transformation of cells.

The latest and most commonly used method is the biolistic method (also known as the gene-gun method). The gene gun injects cells with genetic information using a heavy metal element bullet, like tungsten, coated with plasmid DNA. The gene gun can be used on any type of cell and is not limited to transforming genomes in the nuclei. This process is highly uncertain in the sense that the gene may be introduced in an undesirable location within the plant genome which may result in adverse effects. Also, multiple copies of the gene may be inserted, fragments of genes from the vector may get associated with the trans-gene, and mainly, transformation-induced mutations like rearrangement, deletion and replication of the plants own genes are sometimes observed.

In the vector method, the gene of interest is introduced directly into the plant genome through viral vectors. When the virus integrates into the plant genome as a part of its natural replication cycle, it takes with it the newly engineered portion that expresses the required protein that induces a new trait in the plant. Another method involves using the bacterium, Agrobacterium tumifaciens, as the vector for the DNA. Agrobacterium is widely used to modify sugar beet, oilseed rape, maize and rice plants. Like viruses, it has the ability to insert DNA directly into the plant genome.

The plasmid method involves inserting the gene of interest into a plasmid – a small DNA molecule that is capable of independent replication in a bacterial cell. This is done by cutting open the plasmid DNA by using certain restriction enzymes and introducing the DNA sequence of the required trait. This plasmid DNA with the new additional sequence is then introduced into a culture of live bacteria, which starts to express the desired proteins.

Scientific, Social and Ethical Issues

As mentioned before, there is a high degree of uncertainty and inaccuracy in the techniques used to genetically modify organisms. One cannot disregard the implications of the genetic modification processes after having studied the molecular aspects of gene positioning and gene silencing techniques. The science of GM crops is still at a comparatively early stage, as the detailed function and significance of most plant genes are still unknown. It is quite certain that GM crops need to be grown, consumed and analysed for a long period of time in order to draw scientific conclusions about their safety.

Some of the main issues of concern for human health include – the possibility of allergenicity, gene transfer and outcrossing. An allergenic protein may be induced during modification of the plant. The Food and Agricultural Organisation of the UN (FAO) and WHO test for allergenicity caused due to GM foods. So far, no cases of allergenicity caused due to GM foods have been reported. Since the effect of GM foods on human health is not adequately understood, concern arises about the use of bacterial or viral DNA during the process and the intake of trans-genes by our body. Outcrossing may occur when the genes from the GM crops moves into conventional crops resulting in an indirect effect on food safety and food security. Proponents of GMOs argue that gene flow occurs widely throughout nature, and the risks of such phenomena should be assessed on a case-by-case basis.

This calls for serious active participation from the scientific community in public policy decision making and contribute their understanding of the possible implications of GM foods during worldwide discussions. Integrity and ethics in research is the forefront of any scientific advancement. The GMO debate today finds itself to be in-between crossfires of scientists claiming both the dangers and benefits of GM crops. One can genuinely question the integrity of scientific research that is grounded in public good, when large corporations influence it.

Another issue of GM foods has to do with the corporate control of the food supply. The majority of the agricultural biotechnology corporations like Monsanto, Syngenta, Calgene and BASF control most of the technology used to create GM crops, including agrochemicals and seeds/tissues needed to grow new plants. These companies, along with those who hold the intellectual property rights, have an influence over the availability and use of GM crops. Advancements in the field to produce safer options to the people require access to this technology. Also, it has been known that most of GM research today only serves large-scale farmers in developed countries. A greater expansion in the field is required so that small-scale farmers in the developing countries also benefit from the technology. Much of the opposition related to this comes from the fact that farmers from the poorer countries will then have to depend on the large corporations to acquire seeds every year as opposed to conventional agriculture, where a part of the seeds produced in one growth year are reserved for the upcoming year.

Labelling of GM foods is another controversial issue. Those in favour of labelling of GM foods believe that it is the consumers’ right to know what’s in their food, especially if health and environmental concerns about some foods have been raised. Some people want to avoid eating animal products (including animal DNA) due to ethical and religious reasons. Opponents of labelling argue that with respect to health effects, there have been no significant differences between GM foods and conventional foods. If allergenicity were detected, the food product would have had the current FDA labelling for that allergenic effect. Other aspects of the labelling controversy deal with expenses and non-available infrastructure (storage, processing, and transportation) of the food industry to segregate GM and non-GM foods2.

Potential benefits and conclusions

GM crops have a considerable potential for improving agriculture, and solve many of the world’s hunger and malnutrition problems. GM crops can help preserve the environment by reducing dependence on herbicides and pesticides. Genetic Engineering technology is our future and cannot be ignored due to its enormous potential benefits. The possible risks and benefits associated with the technology can only be assessed on a case-by-case basis.

An EU funded study looking at the safety of GMOs concluded: “There is, as of today, no scientific evidence associating GMOs with higher risks for the environment or for food and feed safety than conventional plants and organisms3.” The U.S. National Academy of Sciences similarly states: “To date, no adverse health effects attributed to genetic engineering have been documented in the human population4.” Yet there are many challenges that governments of the nations have to face with respect to international policymaking, level of regulation, labelling, risk assessments, liability and safety testing.

We have an ethical obligation to explore the potential of GM crops responsibly and be actively involved in influencing governments during policy making. We must proceed with caution and avoid any unintended harm towards the environment and human health in the process of exploring this powerful technology.

Sources:

  1. Directive 2001/18/EC of the European Parliament and the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90/220/EEC, Official Journal of the European Communities, L106 (2001)
  2. The Scientific American: “GMO Labelling Debate Follow-up” by Kevin Bonham. (Nov 11, 2013)
  3. European Commission – IP/10/1688: Compendium of results of EU-funded research on genetically modified crops. (2010)
  4. National Academy of Sciences. Safety of Genetically Engineered Foods: Approaches to Assessing Unintended Health Effects (2004)