<commit_before>---
title: "Scientific Philosophy and Ethics"
permalink: /open-lab-notebook/scientific-philosophy-ethics/
excerpt: "Key ideas that define my philosophy and ethics of science"
categories:
  - open-lab-notebook
tags:
  - research
  - philosophy of science
  - scientific ethics
---
{% include toc title="Philosophy and Ethics" %}

Below are the philosophies and ethics that shape my research pursuits. They were in large part inspired by the [Green Neuroscience Laboratory](http://greenneuro.org/principles/).  

Please leave your thoughts in the comments below! I'm always open to discussing and improving my understanding and implementation of these ideas.  

## Key ideas

### Movement, perception, and thought are part of the same loop

Movement is fundamental to the workings of the brain. It is clear from an evolutionary perspective that nervous systems developed as a tool for navigating unknown, complex environments. In turn, nervous systems adapt and change in response to the environments with which they interact, including the bodies through which this interaction is implemented; thus, cognition emerges from the interplay between brains, bodies, and the world. Taking all three into account is essential to understanding movement, perception, and thought. These loops are hard to describe in the current "feed-forward" biased language used by most neuroscientists, and a thoughtful re-examination can make our metaphors more useful. 

### Empathetic animal research 

Neuroscience research has made us increasingly aware of both the influence of the environment on the brain, and the intimate similarities between human nervous systems and the nervous systems of other animals. The basic fundaments of biology also tell us that all living things are made from different combinations of the same five molecules (Adenine, Cytosine, Guanine, Thymine, and Uracil). We are starting to find that even invertebrate animals use abilities and processes that we once thought only vertebrates could use. I want to prioritize deep respect for all living systems in my pursuit of greater understanding. As a starting point, I do not use a research methodology on any species unless it is currently considered ethical to use that method in humans. I want to develop tools and techniques that enable scientifically powerful observations of freely moving animals living in playful and enriching habitats. 

### Holistic and non-fatalistic approach

"Nature vs. Nurture" is a false dichotomy that does not acknowledge the brain's ability to modify itself. Reductionism can be a powerful tool but requires understanding what is fundamental to the problem you wish to simplify; thus, it cannot yet be applied to the study of emergent properties, nor to connecting patterns of neural activity to natural behaviors at the organismal level. Neural activity is itself dynamic, responsive, and adaptive to the conditions in which it occurs. Brains exist within bodies and cannot be fully understood in disembodied contexts. These ideas not only describe the primary subject of my studies, but also my primary tool of investigation. I want to design my experiments to embrace the full richness of the brain across spatial levels and timescales. I also try to maintain daily practices that improve my awareness, fitness, and flexibility. 

### Field work establishes "ground truth"; Comparative approach checks generalizability

We now have incredible computational and theoretical tools for simulating possible relationships and interactions of neurons -- in fact, they are almost **too** good, in the sense that we can simulate just about every possible situation we can think of. However, not all of these algorithms reflect the solutions honed by evolution in the various life-forms on our planet, because we don't force our algorithms to deal with the same constraints as biological nervous systems that must develop within and adapt to the real world. We are also discovering that biological systems are so robust and adaptive that laboratory animals can learn just about any behaviour that is reinforced. **When it comes to our computational theories and predictive models, current neuroscience is in many ways overwhelmed by too many options.** If we want to understand real-world nervous systems anytime soon, we need to reduce the possible cellular interactions we can simulate and the possible behaviours we can train and test in the lab to the ones that best reflect what we currently know about real-world nervous systems. Field Neuroscience, or the study of nervous systems "in the wild" (as opposed to in the laboratory), can provide powerful "ground truth" data to help us do exactly this reduction. But even amongst real-world nervous systems, the variaty is huge -- and so we need a way to disambiguate general, fundamental characteristics of all nervous systems versus specialized characteristics unique to a particular species. Comparative Neuroscience, or the study of similar functions across a diverse set of relevant species, can provide the frameworks we need to make this distinction. 

### Open, humble, and cooperative research -- or, paradoxes are useful and can co-exist

Mutual respect, non-violent communication, and humility are essential when investigating complex scientific questions; thus, it is also important to call out scientific misconduct, sensationalist publication, and oppressive hierarchies in research organizations. Open and inclusive scientific research can dramatically increase the pace of scientific progress, by motivating more meticulous documentation, better communication between professional science and the general public, and increased cross-pollination of ideas and techniques between disciplines. However, researchers also need safe spaces to make mistakes, report negative results, try radical new approaches, and pursue questions challenging the status quo. I support the open science community by using open source technologies and publishing platforms, and by deliberately designing my projects to bridge science, engineering, humanities, and the arts. At the same time, I work best in small long-term teams, and I believe that modern neuroscientists needs to earnestly discuss the concepts and ideals that define our craft, so that we may better collaborate outside our field. 
<commit_msg>added refs to PCT, humane experimental technique<commit_after>---
title: "Scientific Philosophy and Ethics"
permalink: /open-lab-notebook/scientific-philosophy-ethics/
excerpt: "Key ideas that define my philosophy and ethics of science"
categories:
  - open-lab-notebook
tags:
  - research
  - philosophy of science
  - scientific ethics
---
{% include toc title="Philosophy and Ethics" %}

Below are the philosophies and ethics that shape my research pursuits. They were in large part inspired by the [Green Neuroscience Laboratory](http://greenneuro.org/principles/).  

Please leave your thoughts in the comments below! I'm always open to discussing and improving my understanding and implementation of these ideas.  

## Key ideas

### Movement, perception, and thought are part of the same loop

Movement is fundamental to the workings of the brain. It is clear from an evolutionary perspective that nervous systems developed as a tool for navigating unknown, complex environments. In turn, nervous systems adapt and change in response to the environments with which they interact, including the bodies through which this interaction is implemented; thus, cognition emerges from the interplay between brains, bodies, and the world. Taking all three into account is essential to understanding movement, perception, and thought. These loops are hard to describe and understand using the open-loop causal model currently used to frame most neuroscience experiments. Instead, I would like to design experiments and re-analyze existing data based on the closed-loop control model described by Perceptual Control Theory and the Test for Controlled Variables ([Marken, <NAME>. "You say you had a revolution: Methodological foundations of closed-loop psychology." Review of General Psychology 13.2 (2009): 137.](https://www.researchgate.net/profile/Richard_Marken/publication/232499797_You_Say_You_Had_a_Revolution_Methodological_Foundations_of_Closed-Loop_Psychology/links/574da87108ae8bc5d15bce5f/You-Say-You-Had-a-Revolution-Methodological-Foundations-of-Closed-Loop-Psychology.pdf)).

### Empathetic animal research 

Neuroscience research has made us increasingly aware of both the influence of the environment on the brain, and the intimate similarities between human nervous systems and the nervous systems of other animals. The basic fundaments of biology also tell us that all living things are made from different combinations of the same five molecules (Adenine, Cytosine, Guanine, Thymine, and Uracil). We are starting to find that even invertebrate animals use abilities and processes that we once thought only vertebrates could use. I want to prioritize deep respect for all living systems in my pursuit of greater understanding, in recognition that "the humanest possible treatment of experimental animals, far from being an obstacle, is actually a prerequisite for successful animal experiments" ([Russell, <NAME>, <NAME>, and <NAME>. "The principles of humane experimental technique." (1959)](http://altweb.jhsph.edu/pubs/books/humane_exp/chap1a)). As a starting point, I do not use a research methodology on any species unless it is currently considered ethical to use that method in humans. I want to develop tools and techniques that enable scientifically powerful observations of freely moving animals living in playful and enriching habitats. 

### Holistic and non-fatalistic approach

"Nature vs. Nurture" is a false dichotomy that does not acknowledge the brain's ability to modify itself. Reductionism can be a powerful tool but requires understanding what is fundamental to the problem you wish to simplify; thus, it cannot yet be applied to the study of emergent properties, nor to connecting patterns of neural activity to natural behaviors at the organismal level. Neural activity is itself dynamic, responsive, and adaptive to the conditions in which it occurs. Brains exist within bodies and cannot be fully understood in disembodied contexts. These ideas not only describe the primary subject of my studies, but also my primary tool of investigation. I want to design my experiments to embrace the full richness of the brain across spatial levels and timescales. I also try to maintain daily practices that improve my awareness, fitness, and flexibility. 

### Field work establishes "ground truth"; Comparative approach checks generalizability

We now have incredible computational and theoretical tools for simulating possible relationships and interactions of neurons -- in fact, they are almost **too** good, in the sense that we can simulate just about every possible situation we can think of. However, not all of these algorithms reflect the solutions honed by evolution in the various life-forms on our planet, because we don't force our algorithms to deal with the same constraints as biological nervous systems that must develop within and adapt to the real world. We are also discovering that biological systems are so robust and adaptive that laboratory animals can learn just about any behaviour that is reinforced. **When it comes to our computational theories and predictive models, current neuroscience is in many ways overwhelmed by too many options.** If we want to understand real-world nervous systems anytime soon, we need to reduce the possible cellular interactions we can simulate and the possible behaviours we can train and test in the lab to the ones that best reflect what we currently know about real-world nervous systems. Field Neuroscience, or the study of nervous systems "in the wild" (as opposed to in the laboratory), can provide powerful "ground truth" data to help us do exactly this reduction. But even amongst real-world nervous systems, the variaty is huge -- and so we need a way to disambiguate general, fundamental characteristics of all nervous systems versus specialized characteristics unique to a particular species. Comparative Neuroscience, or the study of similar functions across a diverse set of relevant species, can provide the frameworks we need to make this distinction. 

### Open, humble, and cooperative research -- or, paradoxes are natural and can co-exist

Mutual respect, non-violent communication, and humility are essential when investigating complex scientific questions; thus, it is also important to call out scientific misconduct, sensationalist publication, and oppressive hierarchies in research organizations. Open and inclusive scientific research can dramatically increase the pace of scientific progress, by motivating more meticulous documentation, better communication between professional science and the general public, and increased cross-pollination of ideas and techniques between disciplines. However, researchers also need safe spaces to make mistakes, report negative results, try radical new approaches, and pursue questions challenging the status quo. I support the open science community by using open source technologies and publishing platforms, and by deliberately designing my projects to bridge science, engineering, humanities, and the arts. At the same time, I work best in small long-term teams, and I believe that modern neuroscientists needs to earnestly discuss the concepts and ideals that define our craft, so that we may better collaborate outside our field. 

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