Genetics (only) won’t save us

In November 2020, a news feature in Nature discussed “A fringe theory [that] links microbes in the brain with the onset of dementia” (Figure 1). While it was nice to see that this “fringe” theory is finally being considered worthy of discussion by top journals, the article also highlighted the mainstream view, the one which kept this theory on the fringes for a long time. “But I don’t think it is going to be provable” the article quotes Dr. John Hardy, the father of the amyloid cascade hypothesis, “and I don’t think there is much left that needs to be explained about Alzheimer’s beyond the genetics”, he added. This statement is not only inaccurate, but it also reflects the core framework that has dominated the field of neurodegeneration for the past four decades. This framework emphasizes that nothing more than genetics is needed to understand these diseases, and if we just keep sequencing more people and conducting more genetic studies, the problem will eventually be solved.

Two questions arise here:

1. How did the genetics-only or genetics-first view came to be the prevailing one?

2. Isn’t that true? What else do we need to understand a disease than to understand its genes?

Figure. 1

1. Path to Dominance

To answer the first question, we need to look at the history of science and how it evolved throughout the 20^th century. In the early decades of the 20th-century, physics was the discipline undertaking revolutionary changes and achieving great successes. Starting with Max Plank and Albert Einstein and then via Bohr, Heisenberg, Born, Dirac, Pauli, de Broglie, Schrödinger, and the other pioneers of relativity and quantum mechanics. By the mid-40s, encouraged by the spectacular achievements of the new physics and towards the end of the war, many physicists started utilizing their physical expertise to understand the more complex problems of biology. Notable examples include Erwin Schrödinger writing his influential book (What is life) in 1944 and John von Neumann’s (the father of modern computers) theoretical work on cellular automata and self-reproducing machines. These efforts inspired more physicists such as Linus Pauling, Francis Crick, Rosalind Franklin, and Maurice Wilkins to try to experimentally unravel the molecular foundations of life. Also, the chemists and biochemists who worked on these problems such as Erwin Chargaff, James Watson, Fredric Sanger and Sydney Brenner had an extensive command of the physical basis of the problem they were trying to solve. Physics and physical chemistry were the languages of the age, and you could not expect to have any meaningful contribution to the field - later to be called molecular biology- if you were not proficient in the physicochemical language that governs it.

It worked! The code of life was cracked in 1953, and through the 60s and 70s, nearly all the remaining pieces of the genetic puzzle were found. From deciphering the genetic code to discovering mRNA, tRNA, ribosomes, and a myriad of other components and processes. A spectacular and coherent picture of molecular biology emerged; powerful, beautiful, and clear. This endeavor culminated in the late 70s with the development of genetic engineering (Herbert Boyer and Stanley Cohen) and DNA sequencing (Fredric Sanger and others). Thus, going into the 80s, genetics was queen! From finding the code of life to ushering in the biotechnology revolution, it seemingly explained all that needed to be explained in biology. All that is left to understand living things and cure all diseases is to do more genetics. More sequencing of more species and more genes for more diseases. The foundation was laid; we just need to keep building on top of it. Consequently, the new generation of scientists working at that time was becoming more and more specialized, studying specific genes and genetic pathways or sub-pathways of particular processes or particular diseases. The targets are already set and clear, nothing is hidden, and the goal is who will be there first, who will be the first to find an important gene or genetic pathway for an important process or a devastating disease. It’s not an excursion anymore, it’s just a race!

Gradually, with more sequencing and more specialization, biological research and education were pushed further and further away from their theoretical and physical foundations in information theory and physical chemistry. Genetics became its standalone foundation, with seemingly nothing deeper underneath. Genetic studies were widely considered enough to understand both physiology and pathology. This was the state of thinking when scientists approached the problem of amyloid diseases in the 80’s. It was a given that the solution has to be in genetics. And if not totally in classical genetics, it has to be explained by a quasi-genetic framework of proteins behaving as genes, units of information that can replicate and propagate some kind of biological information. There and then the roots of the genetic-only approach  and the quasi-genetic protein-only hypothesis were laid. Genetics was so established and fundamental that there could not possibly be another way to explain a phenomenon in biology except via genetic or quasi-genetic mechanisms. This strong and firm belief also explains the rather dismissive and exclusionary nature of the genetics-only framework, as expressed by the quote from Dr. John Hardy mentioned earlier “I don’t think there is much left that needs to be explained about Alzheimer’s beyond the genetics” or as expressed by confidently adding the word “only” to the title of the “protein-only” hypothesis, immediately rejecting and invalidating any other way of thinking about the problem. 

But isn’t that correct?  What more than genetics do you need to solve a biological problem?

2. Deeper Foundations

It is very important to remember that genetics is not the most fundamental level of understanding biological phenomena, physics and chemistry are. When approaching a biological problem, especially one of a clearly physical nature such as amyloid protein aggregation, we do not need to start by viewing everything through the lens of genetics. This doesn’t mean excluding genetics, of course not. It just means that priorities need to be rearranged. When dealing with a physical problem, the genetic and biological understanding should follow the physical understanding, not the other way round. Mechanisms of nucleation and phase transformation and principles of thermodynamics should be the core tools and language used to deal with the problem, and genetic and clinical data should be understood within this physical framework. There is no need to invent new terms to describe things that already have accurate terms, models, and equations to describe them in physical chemistry just because they happen to occur in a living organism. The same laws apply within the brain as outside of it. Why use propagation/replication instead of phase-transformation/crystallization, oligomers instead of nuclei, and strains instead of polymorphs? The difference between these terms is not only linguistic but deeply conceptual. Such terms are widely thought to describe entirely new biological concepts, as the Nobel Foundation described the prion concept as “a new biological principle of infection”. The new terms, by bestowing quasi-genetic qualities on aggregating proteins, implied a new biological reality that is different from anything that has been described before, a conceptual breakthrough worthy of the Nobel Prize. However, nearly 40 years after introducing the new concepts “Embarrassingly for the prion field, no definitive structural evidence for these presumptions has come forward… As such, many of the questions raised by Prusiner in 1982—prion structure, mechanism of replication, and drivers of toxicity—are still open”, says the prominent prion researcher Dr. Adriano Aguzzi in a special issue on neurodegeneration in Science Magazine in 2020. 

Embarrassing for the field and sad for the patients and carers, but unfortunately not surprising. The new terms and the concepts they carry infused the field with unnecessary mystery and confusion by virtue of being inaccurate, vague, and lacking grounding in established physicochemical theories. However, there is no need for this self-inflicted damage, and there are better ways to tackle the amyloid problem, only if we agree on which language to use to describe it; thermodynamics.

Thermodynamics sounds like a fancy word, but it is the physical theory that provides, among many other things, the rules that govern the relationship between different states of matter, liquid, solid, and gas. Based on three simple laws and an elegant mathematical structure, it has been frequently referred to as one of the best and most important theories humans have ever come up with. Thus, when dealing with a problem relating to different states of any molecule, including proteins, it is the rules and language of thermodynamics that apply. Again, the same laws apply within the brain as outside of it. Through the lens of thermodynamics, the amyloid phenomenon comes right into focus, no blurriness or confusion. Everything has a name, a law, and an equation. The path has been charted and paved by the likes of Boyle, Boltzman, and Gibbs. We already have theories and tools to accurately name, describe and understand the amyloid phenomenon. All that is needed is to give the physicochemical descriptions the primacy they deserve, and for biologists, geneticists, and clinicians to start using the real language of the field.

Based on the thermodynamic physical framework, the amyloid phenomenon is a simple phase transformation phenomenon similar to what happens billions of times every day from rain or snowfall to the growth of giant crystals in deep caves. It is governed by the second law of thermodynamics, free energy calculations, and the nucleation theory. For well-known thermodynamic reasons the process is biphasic, requiring a nucleation phase followed by an elongation phase. It is also well-established that the nuclei are quite transient and that nucleation can be either spontaneous (homogenous, at very high concentrations) or surface-aided (heterogeneous), the latter being the most common pathway for nucleation. Thus, within this framework, viruses (or other microbes) inducing amyloid aggregation via heterogeneous nucleation (HEN) is not a fringe theory, it is a highly plausible hypothesis based on a quantitative physical mechanism that is more well-defined than anything the protein-only hypothesis managed to find in 40 years. Persistent infections are not uncommon in the brain, and coupled with HEN the case for microbial-induced amyloidosis is very strong. In this picture, genetics is not excluded but included in its rightful place, where overexpression or mutations can facilitate spontaneous nucleation via homogenous nucleation. Moreover, rare infections with preformed amyloid nuclei can also induce aggregation via a seeding mechanism. Thus, the thermodynamic model incorporates all the possible mechanisms of amyloid aggregation, which are not mutually exclusive, and its language describes them clearly and accurately (Fig. 2). The same thermodynamic understanding applies to the mechanism of amyloid toxicity, where the extremely transient intermediates (so-called oligomers) or extremely stable (non-reactive) amyloids are unlikely to significantly contribute to direct toxic effects. Consequently, the mechanism of loss of the native function of the aggregating protein emerges as a far more plausible mechanism of toxicity (as described in a previous post).

Figure 2 from Malberg et al. 2020

Before finishing, I have to comment on the other theory stated in the Nature article that I started the post with; the antimicrobial hypothesis. It contends that the aggregation of Aβ42 serves as an antimicrobial function. Similar to the genetic-only framework, the antimicrobial hypothesis is trying to impose a biological explanation on a physical phenomenon without actual roots in physicochemical mechanisms. And similar to the genetics-only framework it has very limited explanatory power. Does this mean that tau, TDP43, insulin, p53 and the other 40 proteins that form amyloids are all antimicrobial peptides? No need to bestow biological properties on a physical phenomenon unless absolutely necessary. Microbes inducing amyloid aggregation can be fully explained by HEN with no need for antimicrobial justification. The HEN mechanism can apply equally to Aβ, tau, insulin, and all the other aggregating proteins without the need to ignore the extensive literature about their original functions and without forcing them to have new ones.

To conclude, theories should bear the responsibility for their successes and failures. The genetics-only framework, by virtue of being the most supported and funded, is by all means responsible for the current state of a field with total therapeutic sterility. While it might have been justifiable to choose this framework to understand amyloids 40 years ago, the continuous and consistent failures of producing valid mechanisms or therapeutics should prompt us to reconsider this choice. The more fundamental thermodynamic framework offers a clear path with clear mechanisms, all we need to do is to use its language and concepts. It needs to be our guiding principle for analysis and understanding and the basis for judging the validity of different etiologic and pathophysiological mechanisms. If we speak the same language, our different plausibility preferences will converge and hypotheses such as microbial-induced aggregation or loss-of-function toxicity will be more in the mainstream than on the fringes. Rootless mechanismless theories are doomed to fail, and if we want to be as successful as the founders of genetics, we need to go as deep as they did and speak the real language of the problem; physics.