Polychaetous Annelids Research Studies | Natural History Museum of Los Angeles

Research programs in the Polychaete Department span a wide range of topics, including polychaete systematics, philosophy of evolutionary biology, the nature of science, and the evolution versus Intelligent Design
Follow us on FacebookFollow us on TwitterFollow us on FlickrFollow us on YouTubeFollow us on PinterestFollow us on Instagram

Philosophy of Biological Systematics: A course

A slideshow course outlining the fundamentals of the philsophical principles of biological systematics.

Download Slideshow PDF (40MB)

Contact Polychaete Staff

J. Kirk Fitzhugh
Phone:  (213) 763-3233
FAX:       (213) 746-2999

Leslie H. Harris
Collections Manager
Phone:  (213) 763-3234
FAX:       (213) 746-2999

Mailing address:
Research & Collections
Natural History Museum of Los Angeles County
900 Exposition Blvd.
Los Angeles CA 90007

Support Today's Scientists, Inspire Tomorrow's Scientists

When you give to the Museum, you support our scientists' research on the planet's biodiversity. You are also creating tomorrow's scientists. Our teacher resources make each field trip a learning experience, our education outreach brings the science of discovery to schools all over L.A.
Donate to NHMLA Today!

Museum Scientists on Evolution

The Natural History Museum, with its mission to inspire wonder, discovery, and responsibility, recognizes that evolutionary biology is fundamental to understanding biological diversity and is critical for both scientific research and museums. The Museum welcomes people of all beliefs and backgrounds to join us as we explore, through science, the wonders of the natural world.

To see our Evolution Statement in full, click here


Recent Research by J. Kirk Fitzhugh, Ph.D.


My research during the past several years has mainly focused on the inferential foundations of biological systematics, ranging from the relations of observations to systematic hypotheses to the nature of species and all other taxa. Much of the emphasis in this work has been to dispel the popular myth in phylogenetic systematics that its methods for inferring hypotheses are founded on the view of science promoted by the philosopher of science, Karl R. Popper. Popper's influence on twentieth-century science has principally been in the area of testing, often incorrectly referred to as the 'hypothetico-deductive method.' Regrettably, the adoption of hypothetico-deductivism has left many scientists with the view that there only exists a 'logic of justification,' wherein the only component of science worthy of consideration is the testing of theories and hypotheses by way of the deduction of observable consequences. Such an approach has left virtually untouched any consideration of the 'logic of discovery,' that is, the inferential practices applied in all fields of science for the development of theories and hypotheses.

Alternatively, there are other popular schools of thought in which it is contended that biological systematic inference is in some way a matter of statistical or probabilistic estimation. To hold such a position assumes one has critically examined the non-deductive nature of explanatory hypothesis inference. Such has, however, not been the case with respect to systematics, which leaves most statistical, as well as Bayesian, approaches as nothing more than irrelevant curiosities. Indeed, neither the Popperian, statistical, nor Bayesian schools of thought have correctly characterized the inferential structure of systematic hypotheses such that any of them can be defended. The principle reason being that the inferential form to which phylogenetic inference is a member has never been formally addressed throughout the realm of systematists.

By necessity, the logical and inferential bases of biological systematics that I have pursued have lead to addressing such issues as the actual relations of the inferences of systematic hypotheses to their being tested, as well as the nature of coding observations for the purposes of inferring hypotheses that account for those observations. Similarly, the correct relationships of the concepts of 'homology' and 'homoplasy' to systematics hypotheses become clear, and the long-standing issue of whether or not to combine classes of data in the act of inferring hypotheses is readily resolved.


Click here to download the PDF

Among portrayals of evolutionary biology and intelligent design, some evolutionary biologists and organizations have claimed religion and science are compatible, commonly referred to as ‘accommodationism.’ This claim is, from the perspective of science, wholly incorrect. While religion and science are similar in that both seek causal explanations for natural phenomena, this does not render the two approaches compatible or not in conflict. The sciences seek causal understanding by way of theories and hypotheses that ensure understanding is open to critical, empirical evaluation. Reliance on supernatural-based theories and hypotheses are operationally immune to such testing. For religion and science to exist in a complimentary state, religious theories and hypotheses would have to be limited to explaining non-empirical, supernatural phenomena, while scientific theories and hypotheses are applied to natural phenomena. The opportunity for asymmetrical causal overlap is obviated, thus denying the accommodationist position.

MISREPRESENTING SCIENCE: The Intelligent Design Creationism Movement

In addition to my research on systematics, I have recently been investigating errors in the reasoning associated with intelligent design creationism (ID); a school of thought that has received a great deal of press because of the attempts by advocates to present claims; ID is a legitimate scientific alternative to evolutionary biology, and that US public school systems should teach both positions. Since many of the errors with ID have parallels with defenses presented in favor of evolution, it is clear that the public at large needs access to learning how and why scientific inquiry is conducted, and in what ways ID fails drastically to meet accepted scientific criteria. To this end, I have included four short, unpublished articles below.

Evolutionary Biology vs. Intelligent Design: Resolving the Issue


This article addresses some common misconceptions leading to the view that there is a 'debate' between evolutionary biology and intelligent design/creationism. As this paper shows, there actually is no debate at all, but rather a fundamental misunderstanding of how science proceeds as a vehicle for acquiring ever-increasing understanding of the phenomena we perceive around us.

The Mechanics of Testing a Theory: Implications for Intelligent Design


Testing our theories and hypotheses is one of the notable hallmarks of all fields of science. It is the procedure that allows scientists to critically evaluate their claims, as well as the claims of others. Unfortunately, testing is often misunderstood or completely ignored by advocates of intelligent design/creationism. This article outlines the mechanics of testing and the implications this holds for empirically evaluating the utility of intelligent design/creationism as valid, alternative scientific theories.

Science and Religion: Compatible or Incompatible?

It is often said that science and religion are compatible enterprises, given that both have the same goal, which is to acquire understanding of phenomena. In fact, there are several federally funded Web sites on the nature of science and evolution that promote this view. The evolutionary biologist, Stephen J. Gould, has called this point of view “Non-Overlapping Magesteria,” or NOMA. In the brief article here, I point out that while science and religion do have the same goal with regard to natural phenomena, they are not compatible. In fact, they are contradictory according to the basic foundations of science.

"Expelled: No Intelligence Allowed" - How Science Is Misrepresented


The movie, Expelled: No Intelligence Allowed, was released into theaters in the U.S. in 2008. The premise of the movie is that intelligent design/creationism is not being given a fair hearing in the scienfitic community. In this review, I point out some of the common errors made by advocates of intelligent design/creationism that are promoted in the movie.

Recent Publications

  • Fitzhugh, K. 2005a. Les Bases Philosophiques de L’inférence Phylogénétique: Une vue d'ensemble. Biosystema 24:83-105. 
  • Fitzhugh, K. 2005b. The inferential basis of species hypotheses: the solution to defining the term ‘species’. Marine Ecology 26:155-165.  
  • Fitzhugh, K. 2006a. The abduction of phylogenetic hypotheses. Zootaxa 1145:1-110. 
  • Fitzhugh, K. 2006b. The ‘requirement of total evidence’ and its role in phylogenetic systematics. Biology & Philosophy 21:309-351. 
  • Fitzhugh, K. 2006c. The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zoologica Scripta 35:261-286. 
  • Fitzhugh, K. 2006d.  DNA barcoding: an instance of technology-driven science?BioScience 56:462-463. 
  • Fitzhugh, K. 2006e. Response from Fitzhugh. BioScience 56:711. 
  • Fitzhugh, K. 2008a. Fact, theory, test and evolution. Zoologica Scripta 37:109-113. 
  • Fitzhugh, K. 2008b. Abductive inference: implications for ‘Linnean’ and ‘phylogenetic’ approaches for representing biological systematization. Evolutionary Biology 35:52-82. 
  • Fitzhugh, K. 2008c. Clarifying the role of character loss in phylogenetic inference.  Zoologica Scripta 37:561-569. 
  • Fitzhugh, K. 2009a. Between macro and molecular. BioScience 59:85-86.
  • Fitzhugh, K. 2009b. Species as explanatory hypotheses: refinements
    and implications. Acta Biotheoretica 57:201–248.
  • Fitzhugh, K. in prep. ‘Evidence’ for evolution versus ‘evidence’ for intelligent design: parallel confusions.
  • Fitzhugh, K. in prep. Science and the supernatural: compatible or incompatible explanatory realms?