Free the data
Human genome art by humans with genomes
I am more than my genome and my genome is more than me.
— Martin Krzywinski
Watch the video of this project, which features the participants who have a BRCA mutation and their interaction with the piece. The video also highlights the design and construction of the mural.
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I recently took part in a deeply meaningful collaboration of science, art and personal stories of cancer survivors.
Together with Joanna Rudnick and Aaron De La Cruz, we sought to create a work of art that combines the science of cancer genomics and the individuals whose lives are affected by genetic mutations in the BRCA1 and BRCA2 genes, where genomic changes drastically increase one's chances of breast and ovarian cancer.
We wanted to make something that is scientifically accurate, artistically beautiful and emotionally engaging. The complexity of the genome, the multitudes of other genes and possible mutations and the millions of personal stories of hardship and survival were just a few of the elements we wanted to include the the piece.
My role was to provide the scientific direction behind the design and incorporate it into the aesthetic of Aaron De La Cruz, a street artist from San Francisco whose work echoes information, complexity, interaction and continuity. We all have a genome — a different genome. The ways in which our genomes are different is what gives us traits like hair and eye color, but is also what makes some of us predisposed to diseases like cancer.
The mural, which includes elements drawn by the cancer survivors, is part of the Free the Data campaign, which is advocating for an open access model of genome mutation databases so that scientists everywhere can analyze it and help women make informed choices about their breast-cancer risk.
The piece Importance of Data Sharing by Nature Methods illustrated the point:
Imagine you are a physician or researcher and seek to get more confirmation on the clinical impact of particular genetic variants. If your search of public databases comes up empty this does not necessarily mean that nothing is known about the mutations in question. Rather, the information may be locked away as a trade secret in a genetic testing company’s proprietary database.
The New York Times article DNA Project Aims to Make Public a Company’s Data on Cancer Genes captures the current state of the situation.
The mural was constructed on location at InVitae in San Francisco.
A video of the project is available.
This work will be, as far as I know, the first human annotation of mutations in the human genome by humans whose genomes have the mutations. That's quite a term!
I've always been mindful of the necessity of the mingling of art and science. In my work I tried to add things I felt about the science I thought to create work that combines our objective understanding of the world we live in with the subjective experience of living in it. This project, by far, has been the most keenly felt.
The mural was created in San Francisco on Saturday, July 13th, 2013. We are starting with a 11' x 6' wood canvas. These dimensions reflect the ratio of lengths of BRCA1 and BRCA2 proteins (1,863 and 3,418 amino acids, respectively)
The BRCA1 and BRCA2 proteins are drawn on the canvas as straight-line sections.
The locations of the participants mutations are positioned on the protein lines as circles. For individuals with large deletions, the circle is placed at the first affected amino acid. Because BRCA1 is location on the opposite strand (anti-sense), its start on the canvas is on the right.
The rest of the genome is now drawn. Aaron's style is perfect for depicting information and the endless complexity of the genome and its interacting elements. We were careful to include elements that indicate that the story told today is not complete. Millions of others have mutations in thousands of other genes, each potentially life-threatening. Just as the stories of our participants will continue to evolve, other stories are waiting to be told.
Once the "reference" genome is depicted, participants with BRCA1 and BRCA2 mutations will complete the art work by individually marking the positions of their mutations on the art using personalized colors. With Aaron's help, everyone created their own color by mixing primary colors.
From base pair, to genome, to person, to life. All it takes is one tiny change in the genome to change a life forever.
The BRCA1 and BRCA2 lines were placed on the canvas by first pinning two pieces of string, marked with the positions of the mutations.
After drawing the protein lines, it was time to fill the canvas.
Over the next 4 hours, Aaron filled in the canvas with the "rest" of the genome.
Cancer previvors and survivors who have been diagnosed with a mutation on BRCA1 or BRCA2 genes.
Lucy, Karen, Steve, Ghecemy, Joanna, Jill, Lisa, Lynn, Ruth, Jenica, Susan
Aaron De La Cruz's work, though minimal and direct at first, tends to overcome barriers of separation and freely steps in and out of the realms of design, graffiti, and illustration.
The parameters he has chosen to work within actually allow him to free himself and react to the very limitations he has created. This overriding structure and the lack of deliberation while moving within creates a tension when encountering his work due to the almost computer generated grid like systems he creates by unplanned markmaking. The act and the marks themselves are very primal in nature but tend to take on distinct and sometimes higher meanings in the broad range of mediums and contexts they appear in and on.
His work finds strengths in the reduction of his interests in life to minimal information. De La Cruz gains from the idea of exclusion, just because you don't literally see it doesn't mean that its not there.
"https://www.mygenecounsel.com/an-interview-with-filmmaker-joanna-rudnick/">Joanna Rudnick made her directorial debut with the Emmy-nominated In the Family, a deeply personal film about coming to terms with testing positive for the breast cancer gene BRCA1 mutation and following the storylines of other women and families facing the same hard choices. In the Family premiered at Silverdocs in 2008, was broadcast nationally on PBS P.O.V. the same year and was a finalist for the NIHCM Foundation’s Health Care Radio and Television Journalism Award.
Joanna received a master’s degree in Science and Environmental Journalism from New York University and a bachelor’s degree in English from Northwestern University. Joanna loves the opportunity to teach and mentor and served as an adjunct professor at Northwestern University’s Medill School of Journalism in the past.
She has written for several publications including Audubon Magazine, The Artful Mind, The Berkshire Record and Humanities. Before finding her way to the wonderful world of documentaries, Joanna served as an Americorps volunteer, implementing project-based environmental curricula in the San Francisco Public School System.
Joanna is one of the cancer survivors whose mutations are encoded in the art.
Helen Hood Sheer (associate producer)
Fraser Bradshaw (director of photography) (http://www.frazerbradshaw.com)
Jason Joseffer (director of photography) (http://www.jasonjoseffer.com)
Chris Galdes (gaffer)
Anton Herbert (audio)
Sharah Berkovich (production assistant)
Ollie Elliot (panel construction)
Happy 2025 π Day—
TTCAGT: a sequence of digits
Celebrate π Day (March 14th) and sequence digits like its 1999. Let's call some peaks.
Crafting 10 Years of Statistics Explanations: Points of Significance
I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player
Points of Significance is an ongoing series of short articles about statistics in Nature Methods that started in 2013. Its aim is to provide clear explanations of essential concepts in statistics for a nonspecialist audience. The articles favor heuristic explanations and make extensive use of simulated examples and graphical explanations, while maintaining mathematical rigor.
Topics range from basic, but often misunderstood, such as uncertainty and P-values, to relatively advanced, but often neglected, such as the error-in-variables problem and the curse of dimensionality. More recent articles have focused on timely topics such as modeling of epidemics, machine learning, and neural networks.
In this article, we discuss the evolution of topics and details behind some of the story arcs, our approach to crafting statistical explanations and narratives, and our use of figures and numerical simulations as props for building understanding.
Altman, N. & Krzywinski, M. (2025) Crafting 10 Years of Statistics Explanations: Points of Significance. Annual Review of Statistics and Its Application 12:69–87.
Propensity score matching
I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player
In many experimental designs, we need to keep in mind the possibility of confounding variables, which may give rise to bias in the estimate of the treatment effect.
If the control and experimental groups aren't matched (or, roughly, similar enough), this bias can arise.
Sometimes this can be dealt with by randomizing, which on average can balance this effect out. When randomization is not possible, propensity score matching is an excellent strategy to match control and experimental groups.
Kurz, C.F., Krzywinski, M. & Altman, N. (2024) Points of significance: Propensity score matching. Nat. Methods 21:1770–1772.
Understanding p-values and significance
P-values combined with estimates of effect size are used to assess the importance of experimental results. However, their interpretation can be invalidated by selection bias when testing multiple hypotheses, fitting multiple models or even informally selecting results that seem interesting after observing the data.
We offer an introduction to principled uses of p-values (targeted at the non-specialist) and identify questionable practices to be avoided.
Altman, N. & Krzywinski, M. (2024) Understanding p-values and significance. Laboratory Animals 58:443–446.
Depicting variability and uncertainty using intervals and error bars
Variability is inherent in most biological systems due to differences among members of the population. Two types of variation are commonly observed in studies: differences among samples and the “error” in estimating a population parameter (e.g. mean) from a sample. While these concepts are fundamentally very different, the associated variation is often expressed using similar notation—an interval that represents a range of values with a lower and upper bound.
In this article we discuss how common intervals are used (and misused).
Altman, N. & Krzywinski, M. (2024) Depicting variability and uncertainty using intervals and error bars. Laboratory Animals 58:453–456.
Nasa to send our human genome discs to the Moon
We'd like to say a ‘cosmic hello’: mathematics, culture, palaeontology, art and science, and ... human genomes.
