Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Tuesday, February 3, 2026

Combinatorics Summary....

 



 

I realized that I have a combinatorics thread running through my blog across several subjects.  I have been interested in combinatorics since I sent an email to Robert Spitzer on the various combinations of diagnostic criteria.  His only comment was “Interesting”.  Since then, I have commented on a post that purported to discredit psychiatric diagnoses based on combination of diagnostic criteria (too many), a study of the real combinations of major depression diagnoses, and character and word phrase combinations for encryption and password protection.  I went as far as getting dice and using them to construct passphrases of varying length using the Electronic Frontier Foundation (EFF) word list for that purpose.

If you have no experience with combinations or it has been a long time since your college statistics course – dice are a good place to start.  Each die has 6 sides with corresponding numbers. The total combinations possible are 6n, where n = the number of dice rolled at once.  The EFF world list is 6,667 word long and that happens to be 6^5.  So, to generate passphrases – 5 dice are rolled and the corresponding number is looked up on the word list and recorded.  The process is repeated until the desired phrase length is generated.  The only downside to this method is that some sites still insist on additional numbers and special characters.  They can still be inserted in the passphrase, but other systems like hexadecimal may be more convenient.  The advantage to passphrases is that they are theoretically easier to memorize and type without error.  That breaks down with very long phrases.

In biology and medicine, combinatorics can be applied at several levels. Some have more meaning than others.  On this blog, I responded to a paper suggesting that the possible combinations of diagnostic criteria meant that psychiatric diagnoses were meaningless and unscientific.  The lesson from this post is to have an idea of what you are counting and what it means. The total combinations of verbal criteria depend a lot on the phrasing and the total number of criteria whether large or small is not necessarily disqualifying as illustrated in this post.  The combinatorial upper limit can be unrealistically large based on how it is defined and just running the numbers does not mean that all possible combinations will be found.  There also seems to be some magical thinking involved – just because you count something does not say anything about what that means.  It is quite literally an exercise in the map is not the territory. 

I looked at a second paper where the authors looked at a lower number of combinations based on the DSM diagnostic criteria for major depression.  In that case the total number of diagnoses was much lower at 227 combinations.  The authors of that second paper did standardized interviews on 3,800 people and of the 1,566 with major depression – just 10 of those combinations accounted for 50% of the cases.  About ¼ of the possible combinations (57/227) did not occur in any group.  This paper is a stark reminder that just counting things in biology or medicine doesn’t necessarily mean anything.

That brings me to the concept of how we make sense out of the most valid combinatorial explosions in medicine. For me validity is baked into the biology and not a verbal description of things.  The backing for that comes from biological taxonomy and the fact that molecular biology and genomics is solving problems that could not be solved by the verbal description of direct observations in the Linnean tradition.  To that end I am reproducing a table below that is all about the polygenic risk for bipolar disorder. 



Note that in this table the authors are estimating the total possible combinations of 803 polygenes. The theoretical number of possible combinations can be calculated using the formula n! / r!((nr)!,where n represents the number of genetic variants analyzed in a study, and r represents the number of genetic variants per combination. In the case of  SNP genotypes,3^r.the formula is n! / r!(n-r)! ×3^r.  The authors point out that the lowest value for r is 2 but the upper limit is unknown.  They also show how the number of combinations can be limited experimentally.  Of the 57,911,211 combinations found only in patients and not controls they could all be random but there were a significant number of SNPs associated with different groupings in bipolar disorder.    

Using the equations from above in a more readable graphic form:

 

 

Substitution yields the following:

- from the top equation, for 100 variants the theoretical 10-variant combinations would be 1.73 x 1013

- from the bottom equation, for 500,000 SNPs analyzed there would be 2.3 × 1012 two-variant combinations and 3.4 × 1018 three variant combinations.

The application of practical measure includes scanning SNPs for varying combination lengths in the population of interest relative to controls. At lower numbers those combinations can be taken out scanning for longer combinations. A further simplification is to scan only for combinations found in patient populations.  An example of that study is included in the tables below for 803 SNPs in 607 bipolar disorder patients and  1,354 controls. 

Cluster and subgroup analysis is required in very heterogeneous conditions to analyze clusters containing a specific SNP, the distribution of SNP genotypes relative to controls, and cluster selection that contains an SNP for a specific biological function.  Using this kind of analysis 73/609 bipolar disorder patients had these clusters compared to none in the control population. 

While the SNP and variant analysis in 2017 is a good example of combinatoric applications – it did not address the problem of missing heritability.  Missing heritability is the difference between what is observed in familial heritability studies and what is predicted with genetic analysis.  Looking at the predictions from SNP based analysis only a low percentage of familial inheritance was predicted.  That improved with more sensitive analytical techniques that considered additional genetic mechanisms.  The additional mechanisms included SNV (single nucleotide variation), insertions or deletions (indels), SVs (structural variations), CNV (copy number variations), and STR (short tandem repeat (3-5).  Applications that identify all these variations are much more likely to predict the heritability of the pedigree than earlier techniques.  I hope to revisit some of these genetic innovations in an upcoming post about the DSM-6 proposals.

 

George Dawson, MD, DFAPA 

 

References:

1:  Mellerup E, Møller GL. Combinations of Genetic Variants Occurring Exclusively in Patients. Comput Struct Biotechnol J. 2017 Mar 10;15:286-289. doi: 10.1016/j.csbj.2017.03.001. PMID: 28377798; PMCID: PMC5367802.

2:  Koefoed P, Andreassen OA, Bennike B, Dam H, Djurovic S, Hansen T, Jorgensen MB, Kessing LV, Melle I, Møller GL, Mors O, Werge T, Mellerup E. Combinations of SNPs related to signal transduction in bipolar disorder. PLoS One. 2011;6(8):e23812. doi: 10.1371/journal.pone.0023812. Epub 2011 Aug 29. PMID: 21897858; PMCID: PMC3163586.

3:  Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Finocchio A, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ. Comprehensive genome analysis and variant detection at scale using DRAGEN. Nat Biotechnol. 2025 Jul;43(7):1177-1191. doi: 10.1038/s41587-024-02382-1. Epub 2024 Oct 25. PMID: 39455800; PMCID: PMC12022141.

4:  Wainschtein P, Zhang Y, Schwartzentruber J, Kassam I, Sidorenko J, Fiziev PP, Wang H, McRae J, Border R, Zaitlen N, Sankararaman S, Goddard ME, Zeng J, Visscher PM, Farh KK, Yengo L. Estimation and mapping of the missing heritability of human phenotypes. Nature. 2026 Jan;649(8099):1219-1227. doi: 10.1038/s41586-025-09720-6. Epub 2025 Nov 12. PMID: 41225014; PMCID: PMC12851931.

5:  Grotzinger AD, Werme J, Peyrot WJ, Frei O, de Leeuw C, Bicks LK, Guo Q, Margolis MP, Coombes BJ, Batzler A, Pazdernik V, Biernacka JM, Andreassen OA, Anttila V, Børglum AD, Breen G, Cai N, Demontis D, Edenberg HJ, Faraone SV, Franke B, Gandal MJ, Gelernter J, Hatoum AS, Hettema JM, Johnson EC, Jonas KG, Knowles JA, Koenen KC, Maihofer AX, Mallard TT, Mattheisen M, Mitchell KS, Neale BM, Nievergelt CM, Nurnberger JI, O'Connell KS, Peterson RE, Robinson EB, Sanchez-Roige SS, Santangelo SL, Scharf JM, Stefansson H, Stefansson K, Stein MB, Strom NI, Thornton LM, Tucker-Drob EM, Verhulst B, Waldman ID, Walters GB, Wray NR, Yu D; Anxiety Disorders Working Group of the Psychiatric Genomics Consortium; Attention-Deficit/Hyperactivity Disorder (ADHD) Working Group of the Psychiatric Genomics Consortium; Autism Spectrum Disorders Working Group of the Psychiatric Genomics Consortium; Bipolar Disorder Working Group of the Psychiatric Genomics Consortium; Eating Disorders Working Group of the Psychiatric Genomics Consortium; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium; Nicotine Dependence GenOmics (iNDiGO) Consortium; Obsessive-Compulsive Disorder and Tourette Syndrome Working Group of the Psychiatric Genomics Consortium; Post-Traumatic Stress Disorder Working Group of the Psychiatric Genomics Consortium; Schizophrenia Working Group of the Psychiatric Genomics Consortium; Substance Use Disorders Working Group of the Psychiatric Genomics Consortium; Lee PH, Kendler KS, Smoller JW. Mapping the genetic landscape across 14 psychiatric disorders. Nature. 2026 Jan;649(8096):406-415. doi: 10.1038/s41586-025-09820-3. Epub 2025 Dec 10. PMID: 41372416; PMCID: PMC12779569.

 

Graphics Credit:

Table 1 is reused from open access reference 1 above per  CC BY license (http://creativecommons.org/licenses/by/4.0/). 

 

Saturday, June 8, 2024

Philosophy of psychiatry: rhetoric or reality?

 

“If you laid all philosophers end-to-end it would be a good thing.”  Anonymous philosopher lecturing medical students somewhere in the Midwest in the 1980s. 

 

This post is a partial commentary on a paper about the philosophy of psychiatry (1) that was recently published.  Since I am not a philosopher and do not aspire to be one – I thank the authors for commenting on what they believe the key issues and limitations are. Over the years I have written about philosophical conjecture about psychiatry and consider much of it to be serious overreach. This paper will allow me to make some general observations.  The authors in this case have all published previous work on the subject and given the number of co-authors this is considered a state-of-the art review.  The review is open access and can be read at the link in the reference.

In their introduction the authors – consider metaphysical, epistemological, and ethical issues to be critical at the grey zone between medicine and philosophy.  They mention Karl Jaspers as a seminal figure in the field but emphasize their focus in the paper will be on conceptual competence defined as: “the transformative awareness of the ways by which background conceptual assumptions held by clinicians, patients, and society influence and shape aspects of clinical care” (2).  To their credit they explicitly comment on controversies about what the parameters of good philosophy are and whether progress is made over time.

Their first point is on the boundaries of disorder.  They make the usual observations about Kraepelinian and neo-Kraepelinian and conclude that “neo-Kraepelinians (NKs) claimed that precisely defined diagnostic criteria could be used to discover the specific biological causes of psychiatric syndromes and establish psychiatry as a branch of medicine.”  There is plenty of evidence that the NKs were much more sophisticated than that.  From one of their references (3): 

“The medical model is not based on any assumptions about etiology. It can accept social and psychological causes as well as physical and chemical events.  It can accept single causes or multiple causes.  It can even be applied when the etiology is unknown as in many clinical investigations.”

Guze specifies in several places that the diagnosis is for describing what is known about the patient and treatment planning. He suggests that medicine and psychiatry may evolve to provide more information on pathophysiology and testing but does not link it to diagnostic criteria apart from how it might be studied. He does not suggest that biological causes are necessary to establish psychiatry as a branch of medicine – his entire monograph is about why psychiatry is already a branch of medicine.

The next transition is to Insel and the RDoC.  The criticism seems to be that Insel was criticizing biological psychiatry but I doubt that any biological psychiatrist would see translational neuroscience as being inconsistent with a brain and biological centric psychiatry. The field is described as “lurching from one model to another”.  Excluding homosexuality as a diagnosis is given as a notable example of diagnostic controversy rather than psychiatry (specifically Spitzer) getting it right and leading society in general by about 40 years.  There are still plenty of people who have not caught up.

The first main section of their paper is the nature of mental illnesses.  They define strong naturalism as the factual and value free description of a disorder like what occurs in the natural sciences. They equate biological psychiatry with neurobiological dysfunction – even though those psychiatrists clearly had a much more sophisticated view of psychopathology.  I have quoted their reference to Guze above – here is an additional quote from prominent biological psychiatrists of the 20th century:

“It should be emphasized…that the demonstration of…[a catecholamine] abnormality would not necessarily imply a genetic or constitutional, rather than an environmental or psychological, etiology of depression…it is equally conceivable that early experiences of the infant or child may cause enduring biochemical changes and that these may predispose some individuals to depressions in adulthood…[and] any comprehensive formulation of the physiology of affective state will have to include many other concomitant biochemical, physiological, and psychological factors.” (4)

That sounds like pluralism rather than naturalism to me.  There are several additional factors that suggest that the idea of strong naturalism is an exaggeration of the position of late 20th century biological psychiatrists.  Some of those factors include: the concept of heterogeneity in diagnostic categories was widely known at the time, endophenotyping was introduced in 1966 as a purely biological concept (5) that was later applied to medicine and psychiatry (6).  Clinical trialists were certainly aware of heterogeneity and significant problems with recruiting patients into studies based on severity and placebo response.  The general comparison to medical conditions where a significant portion were idiopathic and had speculative pathogenesis and to this day are still diagnosed based on clinical description is an additional factor.  Any intern on medicine or surgery knows pathophysiology and the suggested mechanism of action of medications is typically speculative and no two patients with the same diagnosis are exactly alike.  A key concept in training is that physicians are required to recognize that pattern and make the necessary adaptations.

The authors introduce the definition of strong normativism as basically “no natural, objectively describable set of biological processes that we can characterize as “dysfunctional”, and hence disorder attributions are thoroughly value-laden.”  They do not elaborate – but this definition is clearly counter to the experience of any physician who has treated life threatening or severe illnesses.

Szasz is introduced at that point because of his suggestion that mental illnesses do not exist but rather represent “judgments of deviance based on sociocultural norms”.  They suggest that he is both a strong normativist and a strong naturalist rather than just being wrong.  Szasz’s philosophy (if that is what it was) fails several tests, but for the purpose of this post is probably the best example of controlling the premise rhetoric to prove a point.  The Szasz definition of disease as actual observable pathology allows him to trivialize any condition not meeting that criterion (and there are probably more outside of psychiatry than within) and call it a value judgment.  That is not consistent with diagnostic systems present before him or what historical neuropathologists thought (7).

What follows is a section on the naturalist-normativist debate including a table of the contrasting points. The basic problem with this dichotomy is that the normativist position as described by the authors is such a caricature when compared with medical and psychiatric training that it really cannot be seen as a viable position by anyone but Szasz.  They produce a couple of examples of hybrid positions as though they have never been considered in the past.  The description of Wakefield’s suggestion that dysfunction that is harmful to the individual is required for disorder, but since depression is an evolutionary response to adversity it is not dysfunction.  That ignores empirical research that suggests that it can be both as well as the problems associated with speculation in evolutionary psychology. The discussion of values in the normative model leaves out a lot and ignores psychiatric training. If the goal is to inform psychiatric practice by this kind of debate there are better ways to go. Psychiatrists walk into the room with a patient and their goal is to understand that patient well and treat that patient well. That involves communication skill, developing a therapeutic alliance, therapeutic neutrality, and providing the patient with enough information so that they can provide informed consent.  That interaction is both scientifically and professionally informed.

The next concept the authors discuss is essentialism or the idea that naturally occurring kinds have an evident essence. They acknowledge that when it comes to medical disorders straightforward classification is generally problematic but for some reason it is more problematic for psychiatry. They suggest that:

“If psychiatric classifications such as the DSM and the ICD were demarcating natural kinds, we would expect each diagnosis to correspond to an entity that exists in the structure of the world, independent of human interests.”

That quote misses the mark at a couple of levels.  First, a classification system is really not a diagnosis. It is more of a hypothesis and general locator (8). The diagnosis takes additional information including some of the validators that they minimize in this section. Second, in looking at these features it is obvious that many of the big ones – like mania “exist in the world independent of human interests.”  They have after all been described since ancient times across multiple diagnostic systems – long before there were psychiatrists.  The same is true of melancholia and several other disorders. Granted – there was no DSM back then but I cannot think of better evidence that there are natural kinds by this definition that have been updated. Third, it should be obvious that many disorders are clearly there for research purposes and this is evidenced by the fact that only about 50% of the diagnoses are used on a clinical basis and many psychiatrists attest to the fact that they doubt a single case of specific disorders exist (9,10).  Finally, essentialism in biology became a casualty of evolution.  Prior to Darwin, Linnaeus suggested that species were distinct and unchanging entities created by God.  That is an essentialist position. Evolutionary theory changed all of that because species change based on individual variation and new species occur (11). 

Whenever I read about the philosophical concepts behind what constitutes psychiatric illness and classification – I am always left considering why philosophy is prioritized over biology.  Medicine is after all firmly rooted in human biology.  There is no better evidence than the biochemistry, anatomy, and physiology courses taken in medical school basic science.  Biology provides a framework for both hierarchical organization as well as individual classification of diseases including mental disorders (see lead graphic). Modern taxonomic classifications of both date back to the mid -18th century.

A critical question is whether biological classification has advanced to the point where it is not controversial and purely scientific.  The short answer is no. There is ample evidence that the taxonomy of living organisms is problematic and there are ongoing controversies over the past 50 years.  Although species is a fundamental organizational concept in the field of biology that has not prevented the proliferation of up to 24 different species concepts in recent times (12).  Why would medicine be expected to have a more clearly defined classification system than biology?

Rather than comment on the remaining sections that I am sure that I also have problems with – I am going to introduce and idea that I have not seen written about anywhere.  If you read this an think I am wrong please let me know and send references.  That idea is the application of biological theory to psychiatry. Medicine and psychiatry are after all firmly based in human biology and human biology is a subset of biology in general.  When you attend medical school and complete all the basic science training this basic fact is explicit. There is not much discussion of other organisms unless they happen to be pathogens.  There is also not much discussion of the levels of organization in human biology and the implications that has for medicine.

What does the tremendous complexity of biology have to do with psychiatry? It is evident that various mechanisms make it very difficult to classify biological organisms.  That has resulted in many species concepts and that array of concepts has complicate taxonomy at a time when the biodiversity of the planet remains inadequately characterized. Psychiatry is operating only in one species by the same mechanisms that complicate biology at all levels also complicate biology.  To the purpose of this essay the critical question is why they currently seem less important than the increasing presence of philosophy in psychiatry. Frequently the justification seems to be the old quote about “carving nature at the joints.”  Does that mean we philosophize about it and maintain endless arguments?  Or does it mean we consider that human beings and their mental disorders are based in human biology and try to make sense of it by studying biological principles.  And by biological principles – I don’t mean the typical jargon of biological psychiatry used by critics. I mean theoretical biology practiced by biologists.      

I want to touch on just two concepts from biology that have implications for psychiatric controversies.  The first are the classification systems in biology and the second is stochastics.  There are any number of authors offering descriptions about how psychiatry has evolved in the last 200 years. That generally tracing the origins back to 19th century European schools of thought and bringing those threads forward.  The focus is generally on nosology including diagnostic systems, treatment settings, and how treatments evolved.  The brief discussion of biological classification here touches on a large literature that has been ignored by medicine and psychiatry.  In the debate of categorical versus dimensional diagnoses and the various philosophical labels a significant number of biological classifiers have been left out.

If I am correct what might have caused this significant omission? First, the focus of medicine has been description based on clinical findings.  I have used this characterization previously:

"For several thousand years physicians have recorded observations and studies about their patients.  In the accumulating facts they have recognized patterns of disordered bodily functions and structures as well as forms of mental aberration.  When such categories were sufficiently distinctive, they were termed diseases and given specific names. “

DeGowan and DeGowan, Bedside Diagnostic Examination. 1976, p 1

That has been the historical and primary focus of medicine. Interest in pathogenesis happened in the 19th century but even then, there were conditions that that escaped that classification.  There has been progress there are still many conditions with no clear pathophysiology and even fewer medications where the mechanism of action is known. One of the primary reasons is that medicine has been based on reductionist biology and even though advances have been made it seems to have reached its limit. What do I mean by reductionist biology?  Simply put it means breaking down complex systems to component parts and studying those parts independently.  In current jargon it has also been referred to as a bottom-up approach.  Second – biological psychiatry is biological in the reductive scientific sense and it needs to be biological in the integrative sense. All biology is not reductive (17,18) – but much of the philosophy I have read seems to think so.  Reductive approaches have led to discrete research programs that produce highly speculative connections to psychiatric disorders. We end up with biological psychiatry as neurochemistry -> neuroendocrinology -> neuroimaging -> genomes, connectomes, proteomes, transcriptomes, metabolomes, etc without any clear underlying connection to all human biology.  Systems biology or network medicine approaches have been used on only a partial basis so far.  Third, rather than make a truly biological connection the field seems to have been sidetracked by philosophy.  Much of that philosophy has been around for 50 years or more and seems satisfied with the role of asking questions and never really providing much of an answer.  Much of the philosophy is vague and untestable.  A secondary role seems to be the criticism of psychiatry with a dependence more on political rhetoric than reality.

Conclusion:

When philosophers criticize medicine and psychiatry, they frequently use the term constructs.  From a rhetorical perspective not, all constructs are alike.  In medicine and biology there needs to be at least some real-world observable basis.  

Rather than strong arguments for philosophy in psychiatry – the authors have argued strongly. I have tried to elucidate the rhetoric involved since my observation is that is the nature of most philosophical arguments directed at psychiatry.  The curious aspect is that most people do not even consider this when reading philosophers commenting on psychiatry.  I sent one of my papers to a friend who has been a psychiatrist as long as I have and he told me that he never considered it an area for analysis. I hope that some of the comments here are useful in considering these arguments and why they should not be blindly accepted.

It seems that in all the philosophical criticism and discussion of psychiatry, van Fraassen's empirical adequacy has been ignored (16, 17).  The reasons for that may be less than obvious.  Van Frassen basically states that an empirically adequate model is just that – it is not a comment on the truth of existence or not.  There is a question of whether the model must be based on direct observation.  The criteria for mental disorders require reporting subjective states that are not directly observable. Van Fraassen’s theory includes the outcomes of experiments and isomorphic models – both of which apply to work in psychiatric nosology. The lack of comment on Van Fraasen’s approach is critical because it reflects how psychiatrists are actually trained and directly counters arguments about positivism and realism. Some references suggest that what appear to be diametrically opposed arguments in philosophy are just sustained with no resolution and that is a significant limiting factor when considering what psychiatrists need to know.           

Not all biology is reductionist and not all philosophy is useful.  Empirical adequacy and biological complexity are the future of psychiatry.

 

George Dawson, MD, DFAPA

 

References:

1:  Stein DJ, Nielsen K, Hartford A, Gagné-Julien AM, Glackin S, Friston K, Maj M, Zachar P, Aftab A. Philosophy of psychiatry: theoretical advances and clinical implications. World Psychiatry. 2024 Jun;23(2):215-232. doi: 10.1002/wps.21194. PMID: 38727058; PMCID: PMC11083904.

2:  Aftab A, Waterman GS. Conceptual competence in psychiatry: recommendations for education and training. Acad Psychiatry 2021;45:203-9.

3: Guze SB. Why psychiatry is a branch of medicine. Oxford: Oxford University Press, 1992. p. 38.

4:  Schildkraut JJ, Kety SS. Biogenic amines and emotion. Science. 1967;156 (3771):21-37.

5:  John B, Lewis KR. Chromosome variability and geographic distribution in insects. Science. 1966 May 6;152(3723):711-21. doi: 10.1126/science.152.3723.711. PMID: 17797432.

6:  McGuffin P, Farmer A, Gottesman II. Is there really a split in schizophrenia? The genetic evidence. Br J Psychiatry. 1987 May;150:581-92. doi: 10.1192/bjp.150.5.581. PMID: 3307978.

7:  Pies R.  Did Szasz Misunderstand Virchow’s Concept of disease? Psychiatric Times. Feb 21, 2024.  https://www.psychiatrictimes.com/view/did-szasz-misunderstand-virchow-s-concept-of-disease

8:  Kendler KS. The Phenomenology of Major Depression and the Representativeness and Nature of DSM Criteria. Am J Psychiatry. 2016 Aug 1;173(8):771-80. doi: 10.1176/appi.ajp.2016.15121509. Epub 2016 May 3. PMID: 27138588.

9:  Munk-Jørgensen P, Najarraq Lund M, Bertelsen A. Use of ICD-10 diagnoses in Danish psychiatric hospital-based services in 2001-2007. World Psychiatry. 2010 Oct;9(3):183-4. doi: 10.1002/j.2051-5545.2010.tb00307.x. PMID: 20975866; PMCID: PMC2948730. 

10:  Müssigbrodt H, Michels R, Malchow CP, Dilling H, Munk-Jørgensen P, Bertelsen A. Use of the ICD-10 classification in psychiatry: an international survey. Psychopathology. 2000 Mar-Apr;33(2):94-9. doi: 10.1159/000029127. PMID: 10705253

11:  Hey J.  Genes, categories, and species. NY, NY. Oxford University Press, 2001: p 60-61.

12:  De Queiroz K. Ernst Mayr and the modern concept of species. Proceedings of the National Academy of Sciences. 2005 May 3;102(suppl_1):6600-7.

13:  Mayr E. Biological classification: toward a synthesis of opposing methodologies. Science. 1981 Oct 30;214(4520):510-6. doi: 10.1126/science.214.4520.510.

14:  Mayr E. Biology is not postage stamp collecting. Interview by R. Lewin. Science. 1982 May 14;216(4547):718-20. doi: 10.1126/science.7079730. PMID: 7079730.

15:  Ho CC, Lau SK, Woo PC. Romance of the three domains: how cladistics transformed the classification of cellular organisms. Protein Cell. 2013 Sep;4(9):664-76. doi: 10.1007/s13238-013-3050-9. Epub 2013 Jul 19.

16:  Van Fraassen.  BC.  The Empirical Stance.  New Haven: Yale University Press, 2002.

17:  Monton, Bradley and Chad Mohler, "Constructive Empiricism", The Stanford Encyclopedia of Philosophy (Summer 2021 Edition), Edward N. Zalta (ed.), URL = <https://plato.stanford.edu/archives/sum2021/entries/constructive-empiricism/>.First published Wed Oct 1, 2008; substantive revision Tue Apr 13, 2021

18:  Loscalzo J, Kohane I, Barabasi AL. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol. 2007;3:124. doi: 10.1038/msb4100163. Epub 2007 Jul 10. PMID: 17625512; PMCID: PMC1948102.

19:  Van Regenmortel MH. Reductionism and complexity in molecular biology. Scientists now have the tools to unravel biological and overcome the limitations of reductionism. EMBO Rep. 2004 Nov;5(11):1016-20. doi: 10.1038/sj.embor.7400284. PMID: 15520799; PMCID: PMC1299179.

 

Dedication:  This post is dedicated to my undergraduate biology Professors at Northland College including Lee Stadnyk, Richard Verch, John Brennan, and Mallanpali Rao. I spent many months studying the comparative anatomy and physiology of invertebrates and the taxonomy and population dynamics of sphagnum moss plant species, aquatic invertebrates, and freshwater plankton with these professors and they were the best.  I also had the pleasure of working on Loblolly Pine (Pinus taeda) and Douglas Fir (Pseudotsuga menziesii) species in Don Durzan’s lab at the Institute of Paper Chemistry. Experience in biology is a grounding in the complexity of living organisms.