You’ve probably been exposed to one news headline or another in the recent past (let’s say the last 5 years) that reads something like “SCIENTISTS DISCOVER GENES THAT CAUSE (X).” X, of course, varies massively based on the study itself (and sometimes the bastardisation of said study by media): it can include describing medical conditions such as cancer, autism or congenital diseases; behavioural traits, such as sexual preferences; or broad physical traits, such as the classic problem of the inheritability of height. Unsurprisingly, you may think that trying to find the genes responsible for some traits should be either a) super easy, or b) super hard, depending on your own philosophical preference or the trait in question. So how do these studies come about, anyway?
Earlier in the year, I had made a comment that, as part of the natural evolution of this blog, I would try to change up the writing format every now and then to something a little more personal, emotional and potentially derivative from science. I must confess that this is one of those weeks, as it’s been an emotional rollercoaster for me. So, sorry in advance for the potentially self-oriented, reflective nature of this piece.
Contrastingly, sometimes we might also use genetic information to do the exact opposite. While so many species on Earth are at risk (or have already passed over the precipice) of extinction, some have gone rogue with our intervention. These are, of course, invasive species; pests that have been introduced into new environments and, by their prolific nature, start to throw out the balance of the ecosystem. Australians will be familiar with no shortage of relevant invasive species; the most notable of which is the cane toad, Rhinella marina. However, there are a plethora of invasive species which range from notably prolific (such as the cane toad) to the seemingly mundane (such as the blackbird): so how can we possibly deal with the number and propensity of pests?
Tools for invasive species management
There are a number of tools at our disposal for dealing with invasive species. These range from chemical controls (like pesticides), to biological controls and more recently to targeted genetic methods. Let’s take a quick foray into some of these different methods and their applications to pest control.
The potential secondary impact of biological controls, and the degree of unpredictability in how they will respond to a new environment (and how native species will also respond to their introduction) leads conservationists to develop new, more specific techniques. In similar ways, viral and bacterial-based controls have had limited success (although are still often proposed in conservation management, such as the planned carp herpesvirus release).
The better we understand invasive species and populations from a genetic perspective, the more informed our management efforts can be and the more likely we are to be able to adequately address the problem.
Managing invasive pest species
The impact of human settlement into new environments is exponentially beyond our direct influences. With our arrival, particularly in the last few hundred years, human migration has been an effective conduit for the spread of ecologically-disastrous species which undermine the health and stability of ecosystems around the globe. As such, it is our responsibility to Earth to attempt to address our problems: new genetic techniques is but one growing avenue by which we might be able to remove these invasive pests.
Beyond the apparent ethical and moral objections to the invasive nature of demanding genetic testing for Indigenous peoples, a crucial question is one of feasibility: even if you decided to genetically test for race, is this possible? It might come as a surprise to non-geneticists that actually, from a genetic perspective, race is not a particularly stable concept.
This is exponentially difficult for people who might have fewer sequenced ancestors or relatives; without the reference for genetic variation, it can be even harder to trace their genetic ancestry. Such is the case for Indigenous Australians, for which there is a distinct lack of available genetic data (especially compared to European-descended Australians).
The non-genetic components
The genetic non-identifiability of race is but one aspect which contradicts the rationality of genetic race testing. As we discussed in the previous post on The G-CAT, the connection between genetic underpinning and physicality is not always clear or linear. The role of the environment on both the expression of genetic variation, as well as the general influence of environment on aspects such as behaviour, philosophy, and culture necessitate that more than the genome contributes to a person’s identity. For any given person, how they express and identify themselves is often more strongly associated with their non-genetic traits such as beliefs and culture.
These factors cannot reliably be tested under a genetic framework. While there may be some influence of genes on how a person’s psychology develops, it is unlikely to be able to predict the lifestyle, culture and complete identity of said person. For Indigenous Australians, this has been confounded by the corruption and disruption of their identity through the Stolen Generation. As a result, many Indigenous descendants may not appear (from a genetic point of view) to be purely Indigenous but their identity and culture as an Indigenous person is valid. To suggest that their genetic ancestry more strongly determines their identity than anything else is not only naïve from a scientific perspective, but nothing short of a horrific simplification and degradation of those seeking to reclaim their identity and culture.
The non-identifiability of genetic race
The science of genetics overwhelmingly suggests that there is no fundamental genetic underpinning of ‘race’ that can be reliably used. Furthermore, the impact of non-genetic factors on determining the more important aspects of personal identity, such as culture, tradition and beliefs, demonstrates that attempts to delineate people into subcategories by genetic identity is an unreliable method. Instead, genetic research and biological history fully acknowledges and embraces the diversity of the global human population. As it stands, the phrase ‘human race’ might be the most biologically-sound classification of people: we are all the same.
Over the course of the (relatively brief) history of this blog, I’ve covered a number of varied topics. Many of these have been challenging to write about – either because they are technically-inclined and thus require significant effort to distill down to sensibility and without jargon; or because they address personal issues related to mental health or artistic expression. But despite the nature of these posts, this week’s blog has proven to be one of the most difficult to write, largely because it demands a level of personal vulnerability, acceptance of personality flaws and a potentially self-deprecating message. Alas, I find myself unable to ignore my own perceived importance of the topic.
It should come as no surprise to any reader, whether scientifically trained or not, that the expectation of scientific research is one of total objectivity, clarity and accuracy. Scientific research that is seen not to meet determined quotas of these aspects is undoubtedly labelled ‘bad science’. Naturally, of course, we aim to maximise the value of our research by addressing these as best as can be conceivably possible. Therein, however, lies the limitation: we cannot ever truly be totally objective, nor clear, nor accurate with research, and acceptance and discussion of the limitations of research is a vital aspect of any paper.
The imperfections of science
The basic underpinning of this disjunction lies with the people that conduct the science. Because while the scientific method has been developed and improved over centuries to be as objective, factual and robust as possible, the underlying researchers will always be plagued to some degree by subjectivism. Whether we consciously mean to or not, our prior beliefs, perceptions and history influence the way we conduct or perceive science (hopefully, only to a minor extent).
Additionally, one of the drawbacks of being mortal is that we are prone to making mistakes. Biology is never perfect, and the particularly complex tasks and ideas we assign ourselves to research inevitably involve some level of incorrectness. But while that may seem to fundamentally contradict the nature of science, I argue that is in fact not just a reality of scientific research, but also a necessity for progression.
It cannot be overstated that impostor syndrome is often the result of mental health issues and a high-pressure, demanding academic system, and rarely a rational perception. In many cases, we see only the best aspects of scientific research (both for academic students and the general public), a rose-coloured view of process. What we don’t see, however, is the series of failures and missteps that have led to even the best of scientific outcomes, and may assume that they didn’t happen. This is absolutely false.
The reality is that trying to predict the multitude of factors and problems one can run into when conducting an analysis is a monolithic task. Some aspects relevant to a particular dataset or analysis are unlikely to be discussed or clearly referenced in the literature, and thus difficult to anticipate. Problem solving is often more effective as a reactive, rather than proactive, measure by allowing researchers to respond to an issue when it arises instead of getting bogged down in the astronomical realm of “things that could possibly go wrong.”
Drawing on personal experience, this has led to literal months of reading and preparing data for running models only to have the first dozens of attempts not run or run incorrectly due to something as trivial as formatting. The lesson learnt is that I should have just tried to run the analysis early, stuffed it all up, and learnt from the mistakes with a little problem solving. No matter how much reading I did, or ever could do, some of these mistakes would never have been able to be explicitly predicted a priori.
Why failure is conducive to better research
While we should always strive to be as accurate and objective as possible, sometimes this can be counteractive to our own learning progress. The rabbit holes of “things that could possibly go wrong” run very, very deep and if you fall down them, you’ll surely end up in a bizarre world full of odd distractions, leaps of logic and insanity. Under this circumstance, I suggest allowing yourself to get it wrong: although repeated failures are undoubtedly damaging to the ego and confidence, giving ourselves the opportunity to make mistakes and grow from them ultimately allows us to become more productive and educated than if we avoided them altogether.
Speaking at least from a personal anecdote (although my story appears corroborated with other students’ experiences), some level of failure is critical to the learning process and important for scientific development generally. Although cliché, “learning from our mistakes” is inevitably one of the most effective and quickest ways to learn and allowing ourselves to be imperfect, a little inaccurate or at time foolish is conducive to better science.
Allow yourself to stuff things up. You’ll do it way less in the future if you do.
For anyone who absorbs their news and media through the Internet (hello, welcome to the 21st Century), you would undoubtedly be familiar with a few frustrating and disingenuous aspects of media such as clickbait headlines and targeted advertising. Another one that might aggravate the common reader is Ol’ Reliable, the paywall – blocking access to an article unless some volume of money is transferred to the publisher, usually through a subscription basis. You might argue that this is a necessary evil, or that rewarding well-written pieces and informative journalism through monetary means might lead to the free market starving poor media (extremely optimistically). Or you might argue that the paywall is morally corrupt and greedy, and just another way to extort money out of hapless readers.
Accessibility in science
I’m loathe to tell that you that even science, the powerhouse of objectivity with peer-review to increase accountability, is stifled by the weight of corporate greed. You may notice this from some big name journals, like Natureand Science – articles cost money to access, either at the individual level (e.g. per individual article, or as a subscription for a single person for a year) or for an entire institution (such as universities). To state that these paywalls are exorbitantly priced would be a tremendous understatement – for reference, an institution subscription to the single journal Nature (one of 2,512 journals listed under the conglomerate of Springer Nature) costs nearly $8,000 per year. A download of a single paper often costs around $30 for a curious reader.
Some myths about the publishing process
You might be under the impression, as above, that this money goes towards developing good science and providing a support network for sharing and distributing scientific research. I wish you were right. In his book ‘The Effective Scientist’, Professor Corey Bradshaw describes the academic publishing process as “knowledge slavery”, and no matter how long I spend thinking about this blog post would I ever come up with a more macabre yet apt description. And while I highly recommend his book for a number of reasons, his summary and interpretation of how publishing in science actually works (both the strengths and pitfalls) is highly informative and representative.
There are a number of different aspects about publishing in science that make it so toxic to researchers. For example, the entirety of the funds acquired from the publishing process goes to the publishing institution – none of it goes to the scientists that performed and wrote the work, none to the scientists who reviewed and critiqued the paper prior to publication, and none to the institutions who provided the resources to develop the science. In fact, the perception is that if you publish science in a journal, especially high-ranking ones, it should be an honour just to have your paper in that journal. You got into Nature – what more do you want?
Open Access journals
Thankfully, some journals exist which publish science without the paywall: we refer to these as ‘Open Access’ (OA) journals. Although the increased accessibility is undoubtedly a benefit for the spread of scientific knowledge, the reduced revenue often means that a successful submission comes with an associated cost. This cost is usually presented as an ‘article processing charge’: for a paper in a semi-decent journal, this can be upwards of thousands of dollars for a single paper. Submitting to an OA journal can be a bit of a delicate balance: the increased exposure, transparency and freedom to disseminate research is a definite positive for scientists, but the exorbitant costs that can be associated with OA journals can preclude less productive or financially robust labs from publishing in them (regardless of the quality of science produced).
Manuscripts and ArXives
There is somewhat of a counter culture to the rigorous tyranny of scientific journals: some sites exist where scientists can freely upload their manuscripts and articles without a paywall or submission cost. Naturally, the publishing industry reviles this and many of these are not strictly legal (since you effectively hand over almost all publishing rights to the journal at submission). The most notable of these is Sci-Hub, which uses various techniques (including shifting through different domain names in different countries) to bypass paywalls.
Other more user-generated options exist, such as the different subcategories of ArXiv, where users can upload their own manuscripts free of charge and without a paywall and predominantly prior to the peer-review process. By being publically uploaded, ArXiv sites allow scientists to broaden the peer-review process beyond a few journal-selected reviewers. There is still some screening process when submitting to ArXiv to filter out non-scientific articles, but the overall method is much more transparent and scientist-friendly than a typical publishing corporation. For articles that have already been published, other sites such as Researchgate often act as conduits for sharing research (either those obscured by paywalls, despite copyright issues, or those freely accessible by open access).
You might also have heard through the grapevine that “scientists are allowed to send you PDFs of their research if you email them.” This is a bit of a dubious copyright loophole: often, this is not strictly within the acceptable domain of publishing rights as the journal that has published this research maintains all copyrights to the work (clever). Out of protest, many scientists may send their research to interested parties, often with the caveat of not sharing it anywhere else or in manuscript form (as opposed to the finalised published article). Regardless, scientists are more than eager to share their research however they can.
Civil rights and access to science
There are a number of both empirical and philosophical reasons why free access to science is critically important for all people. At least one of these (among many others) is based on your civil rights. Scientific research is incredibly expensive, and is often funded through a number of grants from various sources, among the most significant of which includes government-funded programs such as the Australian Research Council (ARC).
Where does this money come from? Well, indirectly, you (if you pay your taxes, anyway). While this connection can be at times frustrating for scientists – particularly if there is difficulty in communicating the importance of your research due to a lack of or not-readily-transparent commercial, technological or medical impact of the work – the logic applies to access to scientific data and results, too. As someone who has contributed monetarily to the formation and presentation of scientific work, it is your capitalist right to have access to the results of that work. Although privatisation ultimately overpowers this in the publishing world, there is (in my opinion) a strong moral philosophy behind demanding access to the results of the research you have helped to fund.
Walled off from research
Anyone who has attempted to publish in the scientific literature is undoubtedly keenly aware of the overt corruption and inadequacy of the system. Private businesses hold a monopoly on the dissemination of scientific research, and although science tries to overcome this process, it is a pervasive structure. However, some changes are in process which are seeking to re-invent the way we handle the publishing of scientific research and with strong support from the general public there is opportunity to minimise the damage that private publication businesses proliferate.