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A Course on the Creative Scientific Process

Adapted from: Itai Yanai & Martin Lercher

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Itai Yanai

Professor of Biochemistry at New York University, School of Medicine

Undergraduate degrees in Engineering and Philosophy of Science

PhD in Bioinformatics, Boston University

Postdoctoral fellow at the Weizmann (Israel) and Harvard

Expertise:

  • Single-cell RNA-Seq and spatial transcriptomics.
  • Cancer biology and host-pathogen interactions
  • Evolutionary and developmental biology
  • Computational biology

Professor of Computational Cell Biology at Heinrich Heine University Düsseldorf �(Institute for Computer Science & Department of Biology)

Undergraduate degree in Physics

PhD in Theoretical Physics, Cambridge University

Postdoctoral fellow at the University of Bath and EMBL Heidelberg

Expertise:

  • Computational systems biology
  • Evolutionary genomics
  • Researching the functional evolution of bacteria and plants

Martin Lercher

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Podcast & Editorials

For more, check out our main website:

www.night-science.org

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How does science work?

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Karl Popper and falsification

  • You cannot prove anything to be true; but, you can prove that something is false.

  • What you should be doing then is subjecting any hypothesis to rigorous testing to try to prove that it is wrong, i.e., to falsify it.

  • If you cannot falsify it, then you can say that it’s the best that we have for the moment – but we must always be ready to abandon the idea if it is later falsified.

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“Science in the works has two aspects: what could be called day science and night science

François Jacob (1920-2013), discoverer of

principles of gene regulation

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“Science in the works has two aspects: what could be called day science and night science

“Night science wanders blind. It hesitates, stumbles, recoils, sweats, wakes with a start. Doubting everything, it is forever trying to find itself, question itself, pull itself back together. Night science is a sort of workshop of the possible where what will become the building material of science is worked out.”

François Jacob (1920-2013), discoverer of

principles of gene regulation

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The actual scientific method: �periods of day science & night science

  • Night science allows you to float between ideas.

  • This often happens in associative leaps rather than in logical steps.

Night science is the creative part of science!

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The day/night distinction is shared with the arts

Music:

Art:

Night Music Day Music

Night Art Day Art

Lady Gaga

Frida Kahlo

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Improvisational science

“The fun is always on the other side of a ‘yes’ ”

Martin De Matt

(improvisational theatre instructor)

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Taking a walk with a friend has always been a crucial part of the scientific method

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Rule #1: You need someone you can talk to

The benefits of discussing with a colleague:

  • The other person can make a useful suggestion,
  • Together you can pool information or ideas that you lack individually,
  • A way to uncover errors in reasoning,
  • Receive encouragement about the project,
  • To escape from an established habit of thought.

From Beveridge’s ‘The Art of Scientific Investigation’

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Traditional brainstorming is not ideal

Brainstorming by asking a group of people to suggest ideas on a given problem:

    • Brainstorming this way does not seem to work - at least not for us.
    • The topic gets decided in an ad hoc way.
    • Diffusion of responsibility: In a large group, people tend to stay silent.
    • There appears to be judgement on the ideas.
    • Ideas do not get developed.

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Group Pressure and Conformity

  • Conformity - adjusting one's behavior of thinking to coincide with a group standard.

  • Solomon Asch Experiment (1951): Actors pick the wrong line and then people are coerced by conformity to pick something that they know is wrong:

Alone: <1% made the mistake

In Groups: wrong 33% of the time

  • ‘Group-think’ is a potential problem with brainstorming.

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What is the ideal group size?

Nature, 2019

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Rule #2: Discussions are better when they are one-on-one

Pairs: Working in pairs seems to be ideal.

    • No complicated group dynamics & group think.

A person gets attached to their idea.

    • A second person can help to make progress by making changes.

It’s much more fun to work with another person.

    • A pair can travel further without getting distracted.

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Rule #3: Think of the discussion as an improvisation

Adopt a mindset where you are open to new ideas.

    • Remember that new ideas tend to sound strange and weird when you first hear them.

The ‘Yes, and’ rule of scientific improvisation

    • Same as for �improvisational theatre

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Rule #4: Make the other person look good

  • There is improved creativity for those who practice encouraging statements (related to self-confidence & releasing anxieties) and omit self-incapacitating statements.

  • We all feel stupid �(We all have the imposter syndrome).
  • We can get better into the creative state and reduce our inhibitions if we feel comfortable with our discussion partner.

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Rule #5: It’s not just all talk

  • We need periods of improvisational science with a colleague.

  • But the notion of a lone genius is not entirely a myth. There really is a need for periods of intense work that happens in isolation.

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Improvisational conversations are all around us and yet they may be the hidden part of the scientific method.

  1. small group size, ideally just a pair of people;�
  2. exercising the “yes, and” principle common to other forms of improvisation;
  3. emphasizing an atmosphere of trust – making the other person look good.

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The two languages of science

“If we allow ourselves the license of talking about genes as if they had conscious aims, always reassuring ourselves that we could translate our sloppy language back into respectable terms if we wanted to, we can ask the question, what is a single selfish gene trying to do?”

Richard Dawkins, The Selfish Gene

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“The Selfish Gene” by Richard Dawkins (1976)

“We are all survival machines – robot vehicles blindly programmed to preserve the selfish molecules known as genes”

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Anthropomorphisms are a special type of metaphor

  • To ‘anthropomorphize’ is to give human attributes to nonhuman things.
  • Anthropomorphisms are a special type of metaphors.
  • Some believe that anthropomorphizing can lead to miscommunication and misunderstanding.
    • Clearly genes, proteins, and cells do not “feel” or “want” anything, they are not driven by intentions, but instead move and change based on physical and chemical forces.

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Our brains are wired to adopt the ‘intentional stance’

  • Social cognition was crucial in our evolution.
  • To interact with other people we try to predict their actions.
  • We do this by adopting the intentional stance: we infer beliefs, desires, and intentions
  • Neurological research supports this notion.
  • This is analogous to GPUs, which are optimized for processing image-based information

Spunt et al. J Cogn Neurosci. (2015)

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The language of day science

Day science language is used in:

    • Scientific papers
    • Conference presentations
    • Grant proposals
    • Journal clubs or peer reviews of manuscripts, where we ask if the claims are supported by evidence

Day science starts with a hypothesis that must be expressed in precise, metaphor-free language.

Day science then sets up conclusive experiments with the appropriate controls, and uses statistical methods to assess our confidence in the results

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The language of night science

  • As humans, we require a language permissible to intuition—one that gives us a “feeling” for the phenomenon.
  • In night science language, we are allowed to anthropomorphize freely, helping us to grasp why and how something may be happening.
  • Night science language is not precise, but what we lose in rigor, we gain in intuition.
  • We ask “what does the organism want?” We put ourselves into the shoes of a gene. We ponder the best strategy for a genome in a given situation.
  • We speak in night science language when we are improvising with a colleague.

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Translating between �night science language and day science language

“If we allow ourselves the license of talking about genes as if they had conscious aims, always reassuring ourselves that we could translate our sloppy language back into respectable terms if we wanted to, we can ask the question, what is a single selfish gene trying to do?”

Richard Dawkins, The Selfish Gene

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Night science language can be rephrased in the language of day science.

Night science language:

  • “a cancer gene aims to secure an unfair advantage”

Translated into respectable Day science language:

  • a mutation to a proto-oncogene that causes an increased growth rate of the cells that carry the mutation will over time lead to an increase in the total fraction of body cells that carry the mutation.”

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Translating night science language into respectable day science language

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The language of discovery

  • A truly new idea is born only roughly formed—there may not even be words for it yet.

  • To make that idea falsifiable and thus testable by day science, it needs to be reshaped and refined, and an inexact yet intuitive language is all we initially have for that task. Day science starts with a hypothesis that must be expressed in precise terms.

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Lost in translation

  • Night science language can lead to misunderstandings if we do not clearly distinguish it from the realm of day science.
  • When venturing into night science language in a scientific talk or paper, it should be explicitly noted.
  • An insistence on day science language during a night science discussion will bring the flow of thoughts to a halt.

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What is�the question?

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We have a false sense of the structure of knowledge:

    • We see knowledge as fitting together in a ‘wall of knowledge’.
    • We tend to look for ‘knowledge gaps’

Is our knowledge like a brick wall with some knowledge gaps to be filled in?

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  • We may be forced to build a new wall orthogonal to the first, or even to tear down parts of the existing structure.

  • A truly new question is an unknown unknown - we are neither aware of it nor do we understand it.

A discovery is unexpected and may not fit neatly into our wall

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  • Some questions are so general that they do not provide a new direction towards an answer.

  • Answering them requires a rephrasing (or refocusing) of the original to expose a new aspect - made possible after an insight.

Rephrased questions that led to scientific breakthroughs

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The scientific method:

The perceived (day science) & hidden (night science) view:

“I’m very confused” a student would tell Uri, to which he would reply,

“Oh good - So you’re in the cloud!”

Uri Alon. How to choose a good scientific problem. Mol Cell. 2009

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The perceived (day science) and hidden (night science) view of the scientific method:

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“Is the scientific paper a fraud?”

“I mean that the scientific paper may be a fraud because it misrepresents the processes of thought that accompanied or gave rise to the work that is described in the paper.

That is the question and I will say right away that my answer to it is 'yes'. The scientific paper in its orthodox form does embody a totally mistaken conception, even a travesty, of the nature of scientific thought.”

Peter Medawar

“Father of transplantation"

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Scientific advances…

  • are predictable
  • fill knowledge gaps
  • answer specific questions
  • proceed in a straightforward manner

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Scientific advances…

  • are predictable
  • fill knowledge gaps
  • answer specific questions
  • proceed in a straightforward manner

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The Data-Hypothesis Conversation

“ ‘When someone seeks,’ said Siddhartha, ‘then it easily happens that his eyes see only the thing that he seeks, and he is able to find nothing, to take in nothing. [...] Seeking means: having a goal. But finding means: being free, being open, having no goal.’ ”

Hermann Hesse

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Night science is an attitude!

  • It encourages us to explore and speculate. We ask: What could be hiding here? How would we lure it out?
  • We try look at the data from as many angles as possible.
  • In this mode, we take on a sort of playfulness with the data, comparing everything to everything else.
  • We become explorers, building a map of the data as we start out in one direction, switching directions at crossroads and stumbling into unanticipated regions.

“Not all who wander �are lost”

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Exploration requires a deep understanding of a field

Different backgrounds explain why different researchers discover different things in a dataset.

The same data can lead to different conclusions.

    • In one study, no two teams chose identical work flows to analyze the same dataset, and sets of teams reported contradictory, statistically significant effects.

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Ellen Rothenberg on ‘inhabiting the data’

How do you come up with a new idea?

“I think most of it is inhabiting the data. [...] I know that everybody knows the story about Albert Einstein, imagining himself being a photon. But in a sense, when we look at data sets, that's what we should be doing. Even if we're looking at molecular biology data. If you are this transcription factor in the cell's nucleus: How the hell do you figure out which of the million possible genomic sites you're going to go to in this particular cellular context? [..]

This really helps you identify what I think are really major outstanding problems in one's field.

Ellen Rothenberg

CalTech

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Patternicity, or “just a correlation”?

  • ‘Patternicity’ is the human ability to find patterns and connections.
    • Many patterns may be spurious – �“Correlation is not causation”
    • BUT: finding a new correlation may be �the first glimpse of something new.
  • Data exploration is a generator of correlations �and patterns that can later be tested for causality.
  • Correlations are the domain of night science – �causation is solidified by day science.
  • Science relies on this back and forth between day and night, each overcoming the other’s shortcomings.

Identifying patterns

Testing �for causality

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Beware: Scientists are biased!

  • Psychologists refer to “confirmation bias” as the propensity of viewing new evidence as supporting one's beliefs.

  • Also in science, confirmation bias leads scientists to dismiss or misinterpret publications that contradict their own preconceptions.

  • THUS: We resist confronting contradictions.

Image: The Upturned Microscope

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Interdisciplinarity & Renaissance minds

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Modern science is heavily structured

Our discipline decides:

  • Conferences we attend
  • Journals we publish in
  • Study sections at funding agencies
  • Courses we teach
  • Departments to which we get hired

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The quintessential Renaissance mind:

Leonardo da Vinci

(scientist, artist, philosopher, writer, inventor)

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  1. Optics (white light composition)
  2. Mathematics (calculus)
  3. The three laws of motion (the basic principles of classical physics)
  4. Law of universal gravitation

Isaac Newton’s work transcends any one field

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Fields and subfields are just one way of clustering knowledge.

There are no real boundaries between fields.

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Many scientists were originally trained in a different field.

(In an interdisciplinary project, someone will make the connection.)

Francis Crick

Marie Curie

Training:

Contributed to:

Physics

Physics & Chemistry

Physics

Biology

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Does increased interdisciplinarity really lead to more insights?

There are contradictory results from bibliometric approaches:

    • Not clear that increased interdisciplinarity is necessarily better.�

Different forms of interdisciplinarity:

    • Positive correlation between impact and the variance of the references’ fields;
    • BUT: Lower impact if references too balanced across different fields, or references from very distant fields.�

Those who engage in interdisciplinary research tend to be less productive than the experts.

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Expert’s dilemma: Finding balance between disciplinary day science expertise and interdisciplinary night science creativity.

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Importing an idea from another field

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Exporting an idea to another field

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How can we increase our thinking across disciplines?

Expert by day, Renaissance mind by night

Also, go to an art museum and ask yourself which painting is like your project.

  • Be aware of the distinctions
    • between day and night science
    • between disciplines and scientists.�
  • Read about many things, even if superficial
    • popular science books!�
  • Attend talks that have only a marginal overlap with your work.

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SUMMARY

Day Science Night Science

Mode:

Falsification

Improvisational

Goal:

Hypothesis-testing

Hypothesis-generating

Compartmentalization:

Disciplinary

Interdisciplinary

Language:

Precise

Metaphorical

Logic:

Consistent

Answers

Questions from Contradictions

Puzzle-state:

Solution-testing

Puzzle-switching

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Podcast & Editorials

For more, check out our main website:

www.night-science.org