The Illusion of Separation: A Philosophical Analysis of “Variance Explained”
2050 words
Introduction
“Variance explained” (VE) is a statistical concept which is used to quantify the proportion of variance in a trait that can be accounted for or attributed to one or more independent variables in a statistical model. VE is represented by “R squared”, which ranges from 0 to 100 percent. An r2 of 0 percent means that none of the variance in the dependent variable is explained by the independent variable whereas an r2 of 100 percent means that all of the variance is explained. But VE doesn’t imply causation, it merely quantifies the degree of association or predictability between two variables.
So in the world of genetics, heritability and GWAS, the VE concept has been employed as a fundamental measure to quantify the extent to which a specific trait’s variability can be attributed to genetic factors. One may think that it’s intuitive to think that G and E factors can be separated and their relative influences can be seen and disentangled for human traits. But beneath its apparent simplicity lies a philosophically contentious issue, most importantly, due to the claim/assumption that G and E factors can be separated into percentages.
But I think the concept of VE in psychology/psychometrics and GWAS is mistaken, because (1) it implies a causal relationship that may not exist; (2) implies reductionism; (3) upholds the nature-nurture dichotomy; (4) doesn’t account for interaction and epigenetics; and (5) doesn’t account for context-dependency. In this article, I will argue that the concept of VE is confused, since it assumes too much while explaining too little. Overall, I will explain the issues using a conceptual analysis and then give a few arguments on why I think the phrase is confused.
Arguments against the phrase “variance explained”
While VE doesn’t necessarily imply causation, in psychology/psychometrics and GWAS literature, it seems to be used as somewhat of a causal phrase. The phrase also reduces the trait in question to a single percentage, which is of course not accurate—so basically it attempts at reducing T to a number, a percentage.
But more importantly, the notion of VE is subject to philosophical critique in virtue of the implications of what the phrase inherently means, particularly when it comes to the separation of genetic and environmental factors. The idea of VE most often perpetuates the nature-nurture dichotomy, assuming that G and E can be neatly separated into percentages of causes of a trait. Thus this simplistic division between G and E oversimplifies the intricate interplay between genes, environment and all levels of the developmental system and the irreducible interaction between all developmental resources that lead to the reliable ontogeny of traits (Noble, 2012).
Moreover, VE can be reductionist in nature, since it implies that a certain percentage of a trait’s variance can be attributable to genetics, disregarding the dynamic and complex interactions between genes and other resources in the developmental system. Therefore, this reductionism fails to capture the holistic and emergent nature of human development and behavior. So just like the concept of heritability, the reductionism inherent in the concept of VE focuses on isolating the contributions of G and E, rather than treating them as interacting factors that are not reducible.
Furthermore, we know that epigenetics demonstrates that environmental factors can influence gene expression which then blurs the line between G and E. Therefore, G and E are not separable entities but are intertwined and influence each other in unique ways.
It also may inadvertently carry implicit value judgements about which traits or outcomes are deemed desirable or significant. In a lot circles, a high heritability is seen as evidence for the belief that a trait is strongly influenced by genes—however wrong that may be (Moore and Shenk, 2016). Further, it could also stigmatize environmental influences if a trait is perceived as primarily genetic. This, then, could contribute to a bias that then downplays the importance of environmental factors which would then overlook their importance and potential impact in individual development and behavior.
This concept, moreover, doesn’t provide clarity on questions like identity and causality. Even if a high percentage of variance is attributed to genetics, it doesn’t necessarily reveal the causal mechanisms or genetic factors responsible, which then leads to philosophical indeterminancy regarding the nature of causation. Human traits are highly complex and the attempt to quantify them and break then apart into heat percentages or variances explained by G and E vastly oversimplifies the complexity of these traits. This oversimplification then further contributes to philosophical indeterminancy about the nature and true origins (which would be the irreducible interactions between all developmental resources) of these traits.
The act of quantifying variance also inherently involves power dynamics, where certain variables are deemed more significant or influential than others. This, then, introduces a potential bias that may reflect existing societal norms or power structures. “Variance explained” may inadvertently perpetuate and reinforce these power dynamics by quantifying and emphasizing certain factors over others. (Like eg the results of Hill et al, 2019 and Barth, Papageorge, and Thom, 2020 and see Joseph’s critique of these claims). Basically, these differences between people in income and other socially-important traits are due to genetic differences between them. (Even though there is no molecular genetic evidence for the claim made in The Bell Curve that we are becoming more genetically stratified; Conley and Domingue, 2016.)
The concept of VE also implies a kind of predictive precision that may not align with the uncertainty of human behavior. The illusion of certainty created by high r2 values can lead to misplaced confidence in predictions. In reality, the complexity of human traits often defies prediction and overreliance on VE may create a false sense of certainty.
We also have what I call the “veil of objectivity” argument. This argument challenges the notion that VE provides an entirely objective view. Behind the numerical representation lies a series of subjective decisions, like the selection of variables to the interpretation of results. From the initial selection of variables to be studied to the interpretation of their results, researchers exercise subjective judgments which then could introduce biases and assumptions. So if “variance explained” is presumed to offer an entirely objective view of human traits, then the numerical representation represents an objective measure of variance attribution. If, behind this numerical representation, subjective decisions are involved in variable selection and results interpretation, then the presumed objectivity implied by VE becomes a veil masking underlying subjectivity. So if subjective decisions are integral to the process of VE, then the presumed objectivity of the numerical representation serves as a veil concealing the subjective aspects of the research process. So if the veil of objectivity conceals subjective decisions, then there exists a potential for biases and assumptions which then would influence the quantitative analysis. Thus, if biases and assumptions are inherent in the quantitative analysis due to the veil of objectivity, then the objectivity attributed to VE is compromised, and a more critical examination of subjective elements becomes imperative. This argument of course is for “IQ” studies, heritability studies of socially-important human traits and the like, along with GWASs. In interpreting associations, GWASs and h2 studies also fall prey to the veil of objectivity argument, since as seen above, many people would like the hereditarian claim to be true. So when it comes to GWAS and heritability studies, VE refers to the propagation of phenotypic variance attributed to genetic variance.
So the VE concept assumes a clear separation between genetic and environmental factors which is often reductionist and unwarranted. It doesn’t account for the dynamic nature and influence of these influences, nor—of course—the influence of unmeasured factors. The concepts oversimplification can lead to misunderstandings and has ethical implications, especially when dealing with complex human traits and behaviors. Thus, the VE concept is conceptually flawed and should be used cautiously, if at all, in the fields in which it is applied. It does not adequately represent the complex reality of genetic and environmental influences on human traits. So the VE concept is conceptually limited.
If the concept of VE accurately separates genetic and environmental influences, then it should provide a comprehensive and nuanced representation of factors that contribute to a trait. But the concept does not adequately consider the dynamic interactions, correlations, contextual dependencies, and unmeasured variables. So if the concept does not and cannot address these complexities, then it cannot accurately separate genetic and environmental influences. So if a concept can’t accurately separate genetic and environmental influences, then it lacks coherence in the context of genetic and behavioral studies. Thus the concept of VE lacks coherence in the context of genetic and behavioral studies, as it does not and cannot adequately separate genetic and environmental influences.
Conclusion
In exploring the concept of VE and it’s application in genetic studies, heritability research and GWAS, a series of nuanced critiques have been uncovered that challenge its conceptual coherence. The phrase quantifies the proportion of variance in a trait that is attributed to certain variables, typically genetic and environmental ones. The reductionist nature of VE is apparent since it attempts to distill interplay between G and E into percentages (like h2 studies). But this oversimplification neglects the complexity and dynamic nature of these influences which then perpetuates the nature-nurture dichotomy which fails to capture the intricate interactions between all developmental resources in the system. The concepts inclination to overlook G-E interactions, epigenetic influences, and context-dependents variablity further speaks to its limitations. Lastly, normative assumptions intertwined with the concept thenninteouvde ethical considerations as implicit judgments may stigmatize certain traits or downplay the role and importance of environmental factors. Philosophical indeterminancy, therefore, arises from the inability of the concept of VE to offer clarity on identity, causality, and the complex nature of human traits.
So by considering the reductionist nature, the perpetuation of the false dichotomy between nature and nurture, the oversight of G-E interactions, and the introduction of normative assumptions, I have demonstrated through multiple cases that the phrase “variance explained” falls short in providing a nuanced and coherent understanding of the complexities involved in the study of human traits.
In all reality, the issue of this concept is refuted by the fact that the interaction between all developmental resources shows that the separation of the influences/factors is an impossible project, along with the fact that we know that there is no privileged level of causation. Claims of “variance explained”, heritability, and GWAS all push forth the false notion that the relative contributions of genes and environment can be be quantified into the causes of a trait in question. However, we know now that this is false since this is conceptually confused, since the organism and environment are interdependent. So the inseparability of nature and nurture, genes and environment, means that the The ability for GWAS and heritability studies to meet their intended goals will necessarily fall short, especially due to the missing heritability problem. The phrase “variance explained by” implies a direct causal link between independent and dependent variables. A priori reasoning suggests that the intracacies of human traits are probabilistic and context-dependent and it implicated a vast web of bidirectional influences with feedback loops and dynamic interactions. So if the a priori argument advocates for a contextual, nuanced and probabilistic view of human traits, then it challenges the conceptual foundations of VE.
At the molecular level, the nurture/nature debate currently revolves around reactive genomes and the environments, internal and external to the body, to which they ceaselessly respond. Body boundaries are permeable, and our genome and microbiome are constantly made and remade over our lifetimes. Certain of these changes can be transmitted from one generation to the next and may, at times, persist into succeeding generations. But these findings will not terminate the nurture/nature debate – ongoing research keeps arguments fueled and forces shifts in orientations to shift. Without doubt, molecular pathways will come to light that better account for the circumstances under which specific genes are expressed or inhibited, and data based on correlations will be replaced gradually by causal findings. Slowly, “links” between nurture and nature will collapse, leaving an indivisible entity. But such research, almost exclusively, will miniaturize the environment for the sake of accuracy – an unavoidable process if findings are to be scientifically replicable and reliable. Even so, increasing recognition of the frequency of stochastic, unpredictable events ensures that we can never achieve certainty. (Locke and Pallson, 2016)
Mechanisms that Transcend Natural Selection in the Evolutionary Process: Alternatives to Natural Selection
2250 words
Fodor’s argument was a general complaint against adaptationism. Selection can’t be the mechanism of evolution since it can’t distinguish between causes and correlates of causes—so it thusly can’t account for the creation (arrival) of new species. Here, I will provide quotes showing that the claim that natural selection is a mechanism is ubiquitous in the literature—claims that either Darwin discovered the mechanism or claims that it is a mechanism—and that’s what Fodor was responding to. I will then provide an argument combining saltation, internal physiological mechanisms and decimationism and the EES into a coherent explanatory framework to show that there are alternatives to Darwinian evolution, and that these thusly explain speciation and the proliferation of traits while natural selection can’t since it isn’t a mechanism.
Grant and Grant, 2007: “the driving mechanism of evolutionary change was natural selection”
American Museum of Natural History: “Natural selection is a simple mechanism that causes populations of living things to change over time.”
Andrews et al, 2010: “Natural selection is certainly an important mechanism of allele-frequency change, and it is the only mechanism that generates adaptation of organisms to their environments.”
Pianka: “Natural selection is the only directed evolutionary mechanism resulting in conformity between an organism and its environment”
Cottner and Wassenberg, 2020: “This mechanism is natural selection: individuals who inherit adaptations simply out-compete (by out-surviving and out-reproducing) individuals that do not possess the adaptations.”
So natural selection is seen as the mechanism by which traits become fixed in organisms and how speciation happens. Indeed, Darwin (1859: 54) wrote in On the Origin of Species:
“From these several considerations I think it inevitably follows, that as new species in the course of time are formed through natural selection, others will become rarer and rarer, and finally extinct.”
[And some more of the same from authors in the modern day]
“The role of natural selection in speciation, first described by Darwin, has finally been widely accepted” (Via, 2009)
“Selection must necessarily be involved in speciation” (Barton, 2010)
“Darwin’s theory shows how some natural phenomena may be explained (including at least adaptations and speciation)” (SEP, Natural Selection)
“Natural selection has always been considered a key component of adaptive divergence and speciation (2, 15–17)” (Schneider, 2000)
“Natural selection plays a prominent role in most theories of speciation” (Schulter and Nagel, 1995)
So quite obviously, natural selection is seen as a mechanism, and this mechanism supposedly explains speciation of organisms. But since Fodor (2008) and Fodor and Piattelli-Palmarini (2010) showed that natural selection isn’t a mechanism and can’t explain speciation, then there are obviously other ways that evolution happened. There are alternatives to natural selection, and that’s where I will now turn. I will discuss saltation, internal physiological mechanisms and decimationism and then cohere them into a framework that shows how species can arise sans selection.
Explaining speciation
Saltation is the concept of abrupt and substantial changes which lead to the creation of new species, and it challenges phyletic gradualism through natural selection. Instances of sudden genetic alterations along with other goings-on in the environment that lead to things such as directed mutation can eventually result in the emergence of distinct species. Saltation, therefore, challenges Darwinism showing that certain traits can arise quickly, which lead to the emergence of new species within a short time frame. We also have internal physiological mechanisms which play a role in speciation while influencing the development and divergence of traits within biological populations. They don’t rely on external selective pressures—although goings-on in the environment of course can affect physiology—this emphasizes internal factors like developmental constraints, epigenetic modifications and genetic regulatory networks. These can then lead to the expression of novel traits and then on to speciation without the need for external selective forces. And finally decimationism—which emphasizes periodic mass extinction as drivers of evolutionary change—offers another alternative.
Catastrophic events create holes in ecological niches which then allow for the rapid adaptation and diversification of surviving species. So the decimation and recurrent re-colonizing of ecological niches can then lead to the establishment of distinct lineages (species), which then highlight the role of external and non-selective factors in the process of evolution.
So the interaction between saltation, internal physiological mechanisms, and decimationism thusly provides a novel and comprehensive framework for understanding speciation. Sudden genetic changes and other changes to the system can the initiate the development of unique physiological traits (due to the interaction of the developmental resources, and so any change to one resource would cause a cascading change to the system), while internal mechanisms then ensure the stabilization and heritability of the traits within the population. And when this is coupled with environmental upheaval caused by decimation leading to mass extinctions, these processes then contribute to the formation of new species which then offers a framework and novel perspective of the ARRIVAL of the fittest (Darwin’s theory said nothing about arrival, only the struggle for existence), which extends beyond the concept of natural selection.
So if abrupt genetic and other internal changes (saltation) can passively respond to external stimuli and/or environmental pressures, leading to the emergence of distinct traits within a population, and if internal physiological mechanisms influence the expression and development of these traits, then it follows that saltation, coupled with internal physiological mechanisms, can explain and contribute to the rise of new species. If periodic mass extinctions (decimationism) create ecological vacuums and opportunities for adaptive radiation, and if internal physiological mechanisms play a role in the heritability and stability of traits, then it follows that decimationism in conjunction with internal physiological mechanisms can contribute to the speciation of surviving lineages. Also note that all of this is consistent with Gould’s punctuated equilibrium (PE) model.
Punctuated equilibrium was proposed by Gould and Eldgridge as an alternative to phyletic gradualism (Eldgridge and Gould, 1971). It proposes that species evolve rapidly and not gradually. A developmental gene hypothesis also exists for PE (Casanova and Conkel, 2020).
One prediction of PE is rapid speciation events. During periods of punctuated equilibrium, there will be relatively short intervals of rapid speciation which then result in the emergence of new species. This follows from the theory in that it posits that speciation occurs rapidly, concentrated in short bursts, which lead to the prediction that distinct species should emerge more quickly during these punctuated periods. So if species undergo long periods of stasis with occasional rapid change, then it logically follows that new species should arise quickly during these punctuated periods. Seeing that the PE model was developed to explain the lack of transitional fossils, it proposes that species undergo a long period of morphological stasis, with evolutionary changes occurring in short bursts during speciation events, which therefore provides a framework that accounts for the intermittent presence of transitional fossils in the fossil record.
Another prediction is that during periods of stasis (equilibrium), species will exhibit stability in terms of morphology and adaptation. This follows from the theory in that PE posits that stability characterizes a majority of a species existence and that change should occur in quick bursts. Thus, between these bursts, there should be morphological stability. So the prediction is that observable changes are concentrated in specific intervals.
The epigenome along with transposable elements have been argued to be at the heart of PE, and that “physiological stress, associated with major climatic change or invasion of new habitats, disrupts epigenetic silencing, resulting in TE reactivation, increased TE expression and/or germ-line infection by exogenous retroviruses” (Zeh, Zeh, and Ishida, 2009: 715). Further, this hypothesis—that the epigenetic regulation of transposable elements regulates PE—makes testable predictions (Zeh, Zeh and Ishida, 2009: 721). This is also a mechanism to further explain how stress-induced directed mutations occur. Thus, there is an epigenetic basis for the rapid transformation of species which involves the silencing of transposable elements. So calls for an epigenetic synthesis have been made (Crews and Gore, 2012). We, furthermore, know that Lamarckian inheritance is a major mechanism of evolution (Koonin, 2014). We also know that epigenetic processes like DNA methylation contribute to the evolutionary course (Ash, Colot, and Oldroyd, 2021). Such epigenetic mechanisms have been given solid treatment in West-Eberhard’s (2003) Developmental Plasticity and Evolution. (See also West-Eberhard, 2005 on how developmental plasticity leads to the origin of species differences and Wund, 2015 on the impact of phenotypic plasticity on the evolutionary process.)
Integrating the mechanisms into the EES
So in integrating saltation, internal physiological mechanisms, decimationism, epigenetic processes, phenotypic evaluation and directed mutations into the EES (extended evolutionary synthesis), we can then get a more comprehensive framework. Phenotypic plasticity allows organisms to exhibit various phenotypes in response to various environmental cues, so this introduces a broader aspect of adaptability that go beyond genetic change while emphasizing the capacity of populations to change based on what is going on in the immediate environment during development.
Generic drift and neutral evolution also at a role. So beyond the selective pressures emphasized by the modern synthesis, the EES recognizes that genetic changes can occur through stochastic mechanisms which then influence the genetic constitution of a population. Evo-devo then contributes to the synthesis by highlighting the role of developmental processes in evolutionary outcomes. Thus, by understanding how changes in gene regulation during development contribute to morphological diversity, evo-devo therefore provides insight into evolutionary mechanisms which transcend so-called natural selection.
Moreover, the integration of epigenetic inheritance and cultural evolution also extends the scope of the EES. Epigenetic mechanisms can influence gene expression without a change to the DNA sequence, and can contribute to heritability and adaptability. Cultural evolution, then, while acknowledging the power of transmitted knowledge and practices on adaptive success, also broadens our understanding of evolution beyond biological factors. Thus, by incorporating all of the discussed mechanisms, the EES fosters a unique approach in integrating numerous different mechanisms while recognizing that the evolutionary process is influenced by a mixture of biological, environmental, cultural and developmental factors. There is also the fact that the EES has better predictive and explanatory power than the modern synthesis—it also makes novel predictions (Laland et al, 2015).
Conclusion
This discussion has delved into diverse facets of evolutionary theory, showed that natural selection is seen as a mechanism in the modern day, that Darwin and modern day authors see natural selection as the mechanism of speciation, and has considered a few mechanisms of evolution beyond natural selection. Fodor’s argument was introduced to question the applicability of “selection-for” traits, and challenged the notion of natural selection as a mechanism of evolutionary change. Fodor’s argument therefore paved the way for the mechanisms I discussed and opened the door for the reevaluation of saltation, internal physiological mechanisms, decimationism and the EES more broadly in explaining the fact of evolution. So this discussion has shown that we have to think about evolution not as selection-centric, but in a more holistic manner.
There are clearly epigenetic mechanisms which influence speciation on a PE model, and these epigenetic mechanisms then also contribute to the broader understanding of evolution beyond PE. In the PE model, where speciation events are characterized by rapid and distinct changes, epigenetic mechanisms play a crucial role in influencing the trajectory of evolutionary transitions. These epigenetic mechanisms, then, continue to the heritability of traits and the adaptability of populations. These epigenetic mechanisms also extend beyond their impact of speciation within the PE model. So by influencing gene expression in response to environmental cues, epigenetic changes then provide a dynamic layer to the evolutionary process which allow populations to adapt more rapidly to changing conditions. Therefore, epigenetic mechanisms become integral components in explaining evolutionary dynamics which then align with the principles of the EES.
The integration of these concepts into the EES then further broadens our understanding of evolution. So by incorporating genetic drift, phenotypic plasticity, evo-devo, epigenetic inheritance, directed mutation, and cultural evolution, the EES provides a comprehensive framework which recognizes the complexity of evolutionary process beyond mere reductive genetic change. Phenotypic plasticity allows organisms to be adaptively plastic to respond to cues during development and change the course of their development to respond to what is occurring in the environment without relying solely on genetic changes. Genetic drift then introduces stochastic processes and neutral evolution. Evo-devo then contributes to the synthesis by highlighting the role of developmental processes in evolutionary outcomes. Epigenetic inheritance also brings a non-genetic layer to heritability, acknowledging the impact of environmentally responsive gene regulation. Cultural evolution then recognizes the transmission of knowledge and practices within populations as a factor which influences adaptive success. So putting this all together, these integrations then suggests that evolution is a multifaceted interplay of irreducible levels (Noble, 2012) which then challenges natural selection as a a primary or sole mechanism of evolution and as a mechanism at all, since we can explain what natural selection purports to explain without reliance on it.
So if evolutionary processes encompass mechanisms beyond natural selection like saltation, internal physiological mechanisms, decimationism, punctuated equilibrium, and phenotypic plasticity, and if we are to reject natural selection as an explanation for trait fixation and speciation based on Fodor’s argument, and if these mechanisms are an integral part of the EES, then the EES offers a more comprehensive framework in understanding evolution. Evolutionary processes do encompass mechanisms beyond natural selection as evidenced by critiques of selection-centric views and those views that are seen as alternatives to natural selection like saltation, internal physiological mechanisms and decimationism. Thus, by incorporating the aforementioned mechanisms, we will have a better understanding evolution than if merely relying on the non-mechanism of natural selection to explain trait fixation and sp
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