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Entries from August 1, 2020 - August 31, 2020

Thursday
Aug132020

Fact-checking COVID-19 claims

From a recent interview with a fact-checking journalist:

Claim: Alcohol-based hand sanitiser shouldn't be used day after day as it breaks down the first immune barrier of the body: the lipid bacteria of the skin.

Verdict: Misleading. Alcohol-based gels do reduce the number of skin-resident bacteria and can start to cause some damage to the skin with prolonged use, in some individuals. However, the skin barrier is irrelevant to COVID-19, and alcohol-based gels also eliminate viruses from the skin, preventing transmission to surfaces and your face. Overall there is a clear benefit to use frequent hand-washing, and the negatives can be countered with moisturising.

Claim: We can strengthen our immune system in weeks or even days (for young people), which would mean that if one does contract COVID-19, it's more likely going to be a mild case which does not require hospitalisation.

Verdict: False. First of all, it is misleading to talk about "strengthening" the immune system. The immune system could be considered more like taste. You can increase how spicy food is, or increase how sweet food is - both are "strengthening" the taste but mean different things. Different "flavours" of the immune response are optimal in different circumstances, so there is no such thing as a generic increase in how strong the immune system is. It is also completely unclear as to whether we actually want a "stronger" immune response in COVID-19 - there is good evidence that an excessive immune response of one particular "flavour" is causing the immune pathology. We want to train the immune response in a particular direction (e.g. through vaccines) not generically increase its power (even if that was possible, which it isn't).

Claim: A well functioning immune system is dependent on the quality of our intestinal flora. This is why we should avoid eating refined "industrial" food.

Verdict: Half true. There is an interaction between the gut bacteria and the immune system, and this is modified by the food we eat. It is not very well understood, and it is likely too early to say whether the net effect of the consequences is generally good or generally bad. It is certainly too early to say whether it makes a positive or negative effect in the case of COVID-19. As general advice, eating fresh and unprocessed foods, high in vegetables and low is red meat is good health advice, regardless of what it does to the immune system.

Claim: Fasting strengthens the immune system in only 3 days.

Verdict: False. Fasting modifies the immune system slightly, which could be advantageous in some circumstances and detrimental in others. It is a minor effect though, and certainly it would not be advised that someone with symptomatic COVID-19 undergoes extensive fasting. The body needs resources to fight an infection.

Claim: Herbal supplements such as echinacea and elderberry strengthen the immune system in a matter of weeks.

Verdict: False. There are active compounds in all plants, which can modify aspects of the immune system if given in high enough doses in a dish. That does not mean that eating a few pills does anything at all. It is very important for people to understand that supplements and medicines are regulated completely differently. "Supplements" are allowed to make essentially any claim, without any evidence, as long as that claim is vague. This is why you get garbage claims about "immune boosting": they are vague enough that they are legally allowed to be made without evidence. Actual medicines, on the other hand, can only make extremely specific claims that are backed up by evidence. All claims about herbal supplements should essentially be treated as advertising material. 
Claim: Vitamins and minerals strengthen the immune system.

Verdict: Misleading. Vitamins and minerals are different from other supplements. They are needed by the body in extremely low quantities, and if they are absent then health problems arise. For people who are actually deficient, taking vitamins and minerals will improve health, including the immune system. However, almost no one in the developed world is actually deficient, and certainly having a balanced diet of fresh food will give you more than enough of every known vitamin and mineral. Unless you have an exceptionally limited diet, taking these tablets doesn't do anything.  

Claim: Fear is a powerful immunodepressant.

Verdict: Half-true. Anxiety can modify the immune system, and can give poorer health outcomes during some types of infection. The effect is weak to moderate, but it is measurable. This should not be used as an excuse not to spread awareness of the COVID-19 pandemic, however: some degree of anxiety is rational and protective, where it supports valid infection-avoidance behaviours (e.g., hand-washing, wearing a mask, avoiding crowded areas).

Claim: Practicing yoga strengthens the immune system.

Verdict: Misleading. There is nothing special about yoga. There are, however, weak to moderate beneficial effects of exercise and the alleviation of anxiety on infection outcomes. For some people, they may get this through yoga. Others may get it through gardening, or a daily run, or the ritual of a cup of tea. We should look after our mental health, which means cultivating habits that make us happy. The idea that one particular solution like yoga or mediation has any special properties beyond this is completely unsupported. Keep it up if you enjoy it, but it doesn't replace medicine and won't work for every person.
Friday
Aug072020

Unpopular opinion: the scientific publication system is not the problem

Scientific publishing is undergoing radical change. Nothing surprising there, scientific publishing has been constantly evolving and constantly improving. Innovation and change are needed to improve, although not all innovations end up being useful. I'm on record for saying that the DORA approach, for example, is ideologically well meaning, but so little consideration has been made of the practicalities that the implementation is damaging. Open-access is another example: an excellent ambition, however the pay-to-publish model used for implementation turbo-charged the fake journal industry.

I am glad that we have advocates pushing on various reforms to publishing: pre-print, open-access, retractions, innovations in accreditation, pre-registration, replication journals, trials in blind reviewing, publishing reviews, etc. The advocates do seem, to me, to have far too much belief that their particular reform is critical and often turn a blind eye to the potential downsides. That is also okay: the system needs both passionate advocates and dubious skeptics in order to push changes, throw out the ones that don't work and tweak the ones that do work in order to get the best cost/benefit ratio of implementation.

Fundamentally, though, the publication system is not broken. Oh, it is certainly flawed and improvements are needed and welcomed. But even if every flaw was fixed (which is probably impossible: some ambitions in publishing are at heart mutually contradictory) I don't think it will have the huge benefits that many advocates assume. Because at the heart of it, the problem is not the publication system, but the other systems that publishing flows into.

Let's take two examples:

  • Careers. Probably the main reason why flaws in the publishing system drive so much angst is that scientific publication is the main criteria used in awarding positions and grants. So issues with prestige journals, impact factors and so forth have real implications that damage people's lives and destroy careers. DORA is the ambition to not do that, without the solution of an alternative. Perhaps one day we will find a better system (I happen to believe it lies in improving metrics, and valuing a basket of different metrics for different roles, not in pretending metrics don't exist). But even a perfect system (again, probably impossible) won't fix the issue in career anxiety. Because in the end the issue is that the scientific career structure is broken: it is under-funded, built based on short-term perspectives, and operates on the pressure-cooker approach to milking productivity out of people until they break. From a broader perspective, the scientific career structure is not operating in a vacuum - it is part of a capitalist economy which again fuels these anxieties. Why are people so worried about losing their place in the academic pipeline? Because in our economy changing careers is really, really scary. Fixing publishing doesn't actually fix any of those downstream issues.
  • Translation. The other issue that is frequently raised by advocates for publication change are people who are involved in translation, usually commercialisation or medical implementation. Let's take the example of drug discovery. You don't need to go far in order to find people yelling about the "reproducibility crisis" (although the little data they rely on is, ironically enough, not especially reproducible) or animal-mouse translation issues. It would be great if every published study was 100% reproducible and translatable, although I'm rather sanguine about errors in the literature. There is always a trade-off between speed and reproducibility, and I am okay with speed and novelty being prioritised at the start of the scientific pipeline as long as reproducibility is prioritised at the end. Initiatives to improve what is published are welcomed, but flawed publications on drug discovery are only a problem because they feed into a flawed drug development system. Big pharma uses a system where investments are huge and the decision process is rushed, with the decision-making authority invested in a handful of people. The structure of our intellectual property system rewards decisions made early on incomplete information: snap judgements need to be made too early in the development process. This system will create errors and waste money. More importantly, perhaps, it will also miss opportunities. A medicine slowly developed in the public domain via collaborating experts may be entirely unviable commercially and never enter patients.
So I agree that scientific publishing is flawed, and improvements can and should be made. Unlike some, however, I don't see journals and editors as the enemy - I see them actively engaged in improvements. Like science itself, scientific publishing will improve slowly but steadily, with a few false leads and some backtracking needed. I am perhaps just too cynical to believe that "fixing" publishing will change science the way some advocates state: the problems have a deeper root cause at their heart.