Biology to Learn

This is the sixth posts in the things to learn series. See the intro or the last post about biology vs. physics. This post lists interesting questions and topics in biology.

• What is life? 
• What is the basic architecture of a sample single-celled organism?
• How does life resist entropy internally and maintain order?
• Feedback systems: See Book Review: Design Principles of Biological Circuits
• How is energy passed from light to plants to animals, and how is it used by cells? (See also my carbon poem) 

• DNA and Genes
• Expression - How does the genetic message go from DNA to RNA to proteins?
• How do things like genetic dominance work at the chemical level?
• Reproduction - How does DNA replicate? How does it ensure variation? It's almost paradoxical how much effort life spends to preserve DNA and then also to mix it up. 
• Multiple swaps happen during meiosis
• How are traits inherited? (From Mendelian single-gene traits to more complex multi-gene traits)
• Differentiation - How do cells differentiate during fetal development?
• Initial impetus based on amount of fluid detected in egg/fetus, which then sets off chain reaction where genes signal to other genes. (Seems almost recursive. How did this process evolve?)
• A bit on modern techniques for editing DNA
• Old tech to transfer genes from one organism to another
• CRISPR
• Bigger picture of genetic differences. What does it mean that humans share ~50% of their DNA with a banana or 99.9% of their DNA with each other? How much do people differ from each other? What does that mean? How relevant is the non-coding DNA. 
• Seems us humans are not really 99.9% the same. Even just in coding DNA, letter differences change whole words and CNVs repeat words.
• Practical things can one learn from getting your DNA test 
• What genes led humans to be so different than e.g. chimpanzees. How a small number of genes can make a large difference in the brain's development. How non-coding DNA affects things. 

• Evolution
• Quantitative evolution -  Rates of mutations of DNA of different organisms. How long it takes for an adaptive gene to spread in a population. To what extent can the path of evolution be traced?
• The possible origins of the first life
• The role of epigenetics 
• Philosophy of evolution
• See Stanford articles on evolutionary genetics and teleological notions in biology
• What level evolution occurs at and how animals cooperate (see The Selfish Gene)
• Evolutionary psychology - how much actual evidence vs. speculation. Seems in many areas the brain is general purpose and people can adapt without genetic mutations.
• Related: philosophical interpretations of human nature

• The brain
• How can thoughts and memories arise from neurons? (This is understood to a certain extent.)
• How does consciousness work? (Difficult question!)
• How do Buddhist meditative views on consciousness relate to the scientific nature of the brain. (See Why Buddhism is True)
• To what extent are different animals conscious? Very simple animals (e.g. hydras) are not, and mammals appear to be but what about in-between?
• How did and does the brain develop (evolution, culture, nature, nurture)
• What happens to the brain during sleep?
• Why is it so important for health?
• Can dreams be interpreted as random neurons firing?
• To what extent is the brain hardwired when born vs. a system that learns? 
• Brain starts in very flexible state, but people eventually lose the ability to learn things like vision and speech. Some people can control extra fingers (See polydactyly.) What else could be wired to brain? Brain needs to be general purpose to have evolved.
• Computational neuroscience - how does the brain compare to artificial neural networks? Besides direct neurons firing, what else in the brain is used for processing?
• Behavioral neuroscience - To what extent does understanding the physical mechanisms of the brain help with understanding human psychology? In general, can the mind be viewed as a fully operating layer or are there many leaky abstractions?
  
• The human body and practical health
• Digestion and nutrition
• What makes a balanced diet?
• Metabolism rates and and people's weights. How would skinny people have fared in hungrier times? (See also The Hungry Brain)
• Infection and disease
• how bacteria and viruses spread
• how the layers of the immune system works
• how allergies develop and why they're more common now
• Exercise
• Why it's beneficial
• What practices for most benefits?
• How muscles strengthen and weaken 
• Answering health questions - the fundamentals to know + search skills to find answers
• The connection between psychological wellbeing and physical health
• Modern world - evaluating the risks that new substances (e.g. Teflon, BPA) may pose to human health
• Teeth - how cavities develop and best practices for preventing them
• Besides sugar, which foods are most harmful? How long does it take for decaying processes to start occurring? 
• Can one reduce prevent the mouth from being colonized by harmful bacteria?
• Does flossing work in practice? What are alternatives
• What other treatments exist (e.g. Silver diammine fluoride)
• Sleep - what happens in the body during sleep, best practices for sleep
• Big picture topics 
• Big picture view of evolution (See Big History Course or more poetically, The Goddess of Everything Else)
• Numbers in biology (See book.bionumbers.org)
• Patterns in biology (See Scale)

Biology vs. Physics

This is the fifth post in the series on things to learn. See the intro or the last post on learning physics.

The natural sciences are divided into two branches: the physical sciences (primarily physics and its derivatives) and the life sciences (a.k.a biology). Biology is different than physics in many ways, which affect how one learns it:

• Less Math - Math is fundamental to all of physics but it's more incidental in biology. This can make biology easier to learn for many people.
• More complexity - As challenging as physics is, it's ultimately about simple concepts. But biology is about life, which is complicated.
• Textbooks filled with terminology and small details can make learning biology more tedious. However I think there may be a way to focus more on the overall concepts involved than on the exact terminology and details. When learning for general curiosity, you don't need to know every exact term, you can just learn the terms that will be repeated enough to be worth learning. (See XKCD's thing explainer for an exaggerated example of explaining concepts with less terminology.)
• Unknown frontier - Physics has already solved most areas that a layman would be interested in. The current frontier of physics deals with problems that would be hard a non-physicist to relate to, and it would take years of learning to understand them. Meanwhile biology is filled with unsolved questions in every area from neuroscience to nutrition to genetics to diseases, and one encounters these issues right away. 
• Update: this point is debatable since there are unsolved questions in physics that a layman would be interested in.
• Practical - If you're not an engineer you're unlikely to use knowledge of physics for anything practical. But biology topics like nutrition and disease are relevant to living longer and healthier lives.

There are other ways that physics and biology differ:

Inherent or accidental?

It seems that many parts of physics could be intuited based on other principles and couldn't be any other way:

• Falling objects - Galileo argued against the Aristotelian idea of motion (that heavier objects fall faster) not only with experiments but by pointing out the logical paradoxes that would result.
• Inverse-square law - While one could imagine forces decreasing in other ratios, decreasing in proportion to r² seems the most logical since a force radiating out from a point will spread out according to the formula for a sphere's surface (4πr²).
• Relativity - While most people wouldn't intuitively think of Special Relativity, it seems Einstein was able to recognize that it was the "only way" possible. He was able to derive this based on a deep understanding of the implication's of Maxwell's equations, and he may not even have been aware of the Michelson-Morley experiments.

Questions in physics are still resolved through experiments, but maybe this is to demonstrate the truth to those who don't have the right intuitions of the way nature "needs" to be. When Einstein was asked what if the experiments had disproven his theory of General Relativity, he said "then I would have felt sorry for the dear Lord. The theory is correct." While physics cannot just be pure deduction like mathematics, it's the closest one can get. The eventual goal of physics is to find the theory of everything from which everything else is derived.

Biology however deals with the complex messiness of life, and there's many ways to be a living thing. Scientists can may make predictions based on the data they have, but they can't derive how systems "must" be. Living things are "accidental" in the Aristotelean sense of having traits that they happen to have but could lack.

Purpose 

Ancient and medieval physics used teleological explanations as Aristotle emphasized the "final cause" (or purpose) as one of the "four causes" to explain the way things are, and argued against Democritus who rejected it. Modern physics, starting with Francis Bacon, returned to the physics of Democritus and dropped "purpose" from consideration. Since Isaac Newton, the motion of heavenly and earthly bodies is explained with simple physical laws, without reference to any goal or "natural place" of matter. 

Unlike rocks or stars, living things act with purpose. Even a simple bacterium seeks food, evades predators and maintains its internal state. While scientists no longer use theological explanations to explain why organs and organelles have certain functions and designs, these elements still exist and are worthy of explanation. Some use the term teleonomy to distinguish modern explanations of biological purpose from earlier ones.

In short physics is about mathematical explanations for "simple" things from atoms to galaxies, while biology is about the complexity of life, with all its purpose.