Gregory Petsko wrote a small comment in the very last Genome Biology titled Shadows on the wall. A very angry but still contained one, nicely written and important to think about. Here is some of my thoughts about.
Gregory Petsko discusses a question related to what people call "paradigms" and innovation. Paradigm is a word introduced by Thomas Kuhn in his famous and landmark essay The Structure of Scientific Revolutions. For these who are not familiar with Kuhn’s ideas (shame on you!), here is a brief summary.
So, according to Kuhn, science is a social and historical construction: what can be thought and conceptualized in a given time period? It is crystal clear that Newton’s epoch was not the one where he would have had been able of theorizing E = mc². He stresses the importance of not attributing modern modes of thought to historical actors and argues that the evolution of scientific theory does not emerge from the straightforward accumulation of facts, but rather from a set of changing intellectual circumstances and possibilities. To illustrate his idea, he gives several historical examples such as the Copernican revolution.
Further, he explains what are the ingredients and the phases of a scientific revolution. When he talks about ingredients, he introduces the word "paradigm" and the expression "paradigm shift". The former stands for a thought pattern of a scientific contexte, or more practically , for a set of practices that define a scientific discipline at any particular period of time. A detailed definition is given by Kuhn in his book which encompasses the object of observation (what is to be observed), the questions to be asked and to be answered in relation to this object, the way of asking those question (how the questions are structured) and, last but not least, the interpretation of the answers. Taking these into account gives a coherence of the scientific reasoning. Kuhn calls this "normal science", to underline that this is the one every scientists does (is supposed to do, at least).
Now I come to the paradigm shift. So, imagine that anomalies begin happenning (no, no UFO landing on the top of the Eiffel tour). Anomalies are defined as failures of the current paradigm: it cannot explain some observations. Frequently, those anomalies are errors in observations, it can happen that the current paradigm is slightly modified to fit a given observation, etc.: it depends who practice science. The thing is that even if anomalies persist, science practicionners will not stop believing the current paradigm without having an alternative credible one. So, at one moment, some brave scientists will come up with a statement that there is a crisis and go into what Kuhn calls revolutionary science. They will work to make the new paradigm being accepted. Yes, in the beginning it will be hardcore the new paradigm suffering blanks and anomalies because it is still so new. Sometimes, this new paradigm will be a rival to the current one. Naturally, the scientific community will oppose to this new paradigm, and, as Kuhn precises, it should do so: a sane community is the one where one finds bold people and conservative people. There will be some time where both paradigms will be living together and if the challenging paradigm gathers enough observations and facts to get solidified, it will substitute to the old one. Here we have the famous paradigm shift.
I won’t go into the time steps Kuhn describes or more things such as the critics addressed to this book by Popper, Lakatos, Feyerabend. The most important things are above.
So, to come back to Petsko’s paper: his question comes from a quote from Carlo Rotella:
‘In order to thrive, every genre or style needs both visionary innovators and orthodox practitioners. Without the former, it becomes hidebound. Without the latter, it drifts and loses its center.’ But what happens when orthodoxy becomes dogma? What is the fate of innovators when they pose a threat, not to the accepted view, but to the accepted truth?
He opens with Plato’s Allegory of the Cave and discusses various topics such as the belief Obama is muslim whereas he is not as well the fact that "75% of my fellow countrymen believe in angels and less tha 50% believe in evolution, even though the first do not represent reality and the second does". Yes, we all know this: when whatever novelty is considered as heresy, the people who have invested a lot into a status quo transform into witch-hunters. And this is true especially in science even if scientific progress is the fruit of constant challenges to our understanding and belief how things are. And these challenges are precisely what makes us keep on searching: if we consider that something is fully understood, "we lose the drive to explore", as writes Petsko. And he follows:
Of course, many new ideas really are wrong, but it’s when we start to assume that any new idea must be wrong because it doesn’t fit into what we are certain is right that we become obstacles to progress. Skepticism is a good thing, and extraordinary claims really do require extraordinary evidence, but the most exciting time in science is when paradigms fall, shibboleths become signs of stodginess, and everything is up for grabs.
Afterwards, he evokes several paradigms need to be challenged:
- "The idea that a number of highly expressed proteins are ‘natively unfolded’ or ‘intrinsically disordered’ in the cell." He takes as an example the alpha-synuclein, Parkinson’s disease-related protein which represents almost 1% of the protein content of neurons. The question he addresses is: "Do you really believe that 1% of the protein content of a neuron is made up of something with all the structural order of a plate of spaghetti?" This is dubious, however this paradigm is the predominant one in the Parkinson’s research community and it will die hard.
- "The notion that prokaryotic cells are much less organized than eukaryotic cells." This one makes me particularly angry as well. Petsko says that it is somehow on its way out, but I’m afraid many people really think it. And how many times did you read about "higher eukaryotes" in papers? To me, this kind of considerations fall into the scala naturae, you know, the great chain of being established by medieval theologians willing to order the reality. How could a scientist call prokaryotes simple when they are living beings with one unique cell and few genes doing the same work as this model "of organizational complexity and sophistication" mammalian cell is. I agree with Pestko writing that bacteria "may even turn out to be more sophisticated, because they have had make do with a smaller cell volume and fewer genes.".
- "In genome biology, the idea that all projects aimed at gathering massive amounts of data are equally worthwhile." As he says, administrators do consider that this is untrue. Mabe most of the scientists wouldn’t admit it publicly. Data-mining consumes a big part of a funding and projects such as GWAS (the hype and beloved by many genome-wide association studies) are less worth than claimed in the beginning. "We need a balance in the types of science we support and value, but balance is something that seems in short supply these days."…
- "The belief that to model a system is to understand it." This is direct criticism of systems biology. People doing models consider they equate to understanding. But how this could be when instead of taking into account the complexity of a system, a model makes an wonderful shrinkage and is a reduced and oversimplified version of this system? Sometimes, they explain things (fortunately!), but in general models are just a part of something much more sophisticated. So, instead of keeping on assuming (tacitly) "that those who don’t model are archaic reductionists" which "is almost insulting to geneticists and physiologists, who have long understood the importance of considering pathways and processes, interconnected and parallel, in interpreting their experimental data", bioinformaticians and computer science gurus would better do to learn some biology and modesty.
Petsko summarizes these paradigms saying they have in common 2 things: "a sense that it represents the only right view of the world and a coterie of staunch defenders whose reputations and funding depend on acceptance of that view". It is what Kuhn described as well as the time scale of the standpoint change.
His conclusion is extremely important, I paste it as is, please take some time to think about what you just read:
We can all fall into this trap so easily. If we’re not careful, we can mistake our assumptions about reality for reality itself. We can become comfortable, unquestioning, robotic – even dogmatic. We can forget that science only thrives when everything is examined, everything is questioned, and assumptions are not confused with facts. Mavericks are discomforting, often annoying, but without them we risk spending our scientific lives in a cave, never realizing that the things we believe in are merely shadows on the wall.
Petsko GA (2010). Shadows on the wall. Genome biology, 11 (9) PMID: 20863416