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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Null and Alternative Hypotheses01:16

Null and Alternative Hypotheses

The actual hypothesis testing begins by considering two hypotheses. They are termed  the null hypothesis and the alternative hypothesis. These hypotheses contain opposing viewpoints.
The null hypothesis, denoted by H0 is a statement of no difference between the variables—they are not related. This can often be considered the status quo. As  a result if you cannot accept the null, it requires some action.
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Hypothesis: Accept or Fail to Reject?01:17

Hypothesis: Accept or Fail to Reject?

The outcome of any hypothesis testing leads to rejecting or not rejecting the null hypothesis. This decision is taken based on the analysis of the data, an appropriate test statistic, an appropriate confidence level, the critical values, and P-values. However, when the evidence suggests that the null hypothesis cannot be rejected, is it right to say, 'Accept' the null hypothesis?
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Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...
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¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...

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Updated: Jun 3, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Pattern cladism, homology, and theory-neutrality.

Christopher H Pearson1

  • 1Southern Illinois University Edwardsville, SIUE-Philosophy, Box 1433, Edwardsville, IL 62026-1433, USA.

History and Philosophy of the Life Sciences
|April 2, 2011
PubMed
Summary

Pattern cladists aim for theory-neutral biological classification, but this essay questions if observing natural patterns, including homologous traits, truly achieves this goal. The philosophical basis of theory-neutrality in science remains a key debate.

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Area of Science:

  • * Philosophy of Science
  • * Systematic Biology
  • * Evolutionary Biology

Background:

  • * Pattern cladistics proposes theory-neutral classification of biological taxa.
  • * The philosophical concept of theory-neutrality in science is inherently problematic.
  • * Previous critiques of pattern cladistics focused on its commitment to theory-neutrality, not its observational methods.

Purpose of the Study:

  • * To critically examine the claim that observation of natural patterns leads to theory-neutrality in cladistic taxonomy.
  • * To investigate the role of observing homologous traits in achieving theory-neutrality.
  • * To address the under-examined issue of whether observation itself can be theory-neutral.

Main Methods:

  • * Philosophical analysis of the concept of theory-neutrality in scientific observation.
  • * Critical examination of pattern cladists' reliance on observation for taxonomic classification.
  • * Focus on the observation of patterns related to homologous traits within biological taxa.

Main Results:

  • * The philosophical underpinnings of theory-neutral science are questionable.
  • * Observation of patterns, even of homologous traits, may not guarantee theory-neutrality in cladistic taxonomy.
  • * The core assumption that observation equates to theory-neutrality requires deeper scrutiny.

Conclusions:

  • * Pattern cladists' assertion of theory-neutral classification through observation is philosophically contentious.
  • * The reliance on observation, particularly of homologous traits, does not inherently resolve the problem of theory-ladenness in taxonomy.
  • * Further philosophical inquiry is needed into the relationship between observation, pattern recognition, and scientific objectivity in cladistics.