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Enlightened minds, illuminated research

How the AGO’s art inspires researchers at the Princess Margaret Cancer Centre

Enlightened minds, illuminated research

What does scientific discourse have to do with artistic expression? For a research team at the Princess Margaret Cancer Centre, the answer is “everything.”

We once thought of our right and left brains as separate forces responsible for logical and creative thought, respectively. But scientific progress has shown us otherwise, as mental processes require that the whole brain works together in harmony to approach a task.

Just as the corpus callosum brings our hemispheres together as a band of nerve fibres, so too should science and art harmonize — so believes Dr. Mathieu Lupien, a Senior Scientist at the Princess Margaret Cancer Centre. 

Lupien incorporates art into his professional sphere to generate creative discourse between his close-knit team of researchers. He offers a unique approach to team-building by inviting his team to take a stroll through the Art Gallery of Ontario.

Each team member takes the time to walk through and choose a piece of artwork that speaks to them. Lupien then has the team come together as a group to share their chosen piece and engage in dialogue about what inspired them.

“I get to see the world from their perspective and they get to see mine from theirs,” said Lupien in an interview with The Varsity. The process helps the researchers better understand how they see the world through different lenses.

Lupien expresses that this is an exercise in using something creative, like art, to share who we are as scientists. It gives the team a glimpse into each other’s worlds. For example, if a member really enjoys the intricate detail in a piece, we can understand that the fine details they reflect in their own work are something they value. This helps us interpret the work they do in a more meaningful way.

“Our imagination is the only way to explore the unknown,” said Lupien. “We are working in uncharted territory sometimes, so creating an environment that is conducive to open, creative thought is important for our work.”

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How can students integrate art and science into their own research methods?

Lupien describes that translating scientific works in an intelligible way is an art in itself. Science, technology, engineering, and mathematics can be highly complex areas, full of jargon which can be intimidating for many students interested in the field. Using creative expression is one way to translate complexities in an imaginative way.

He demonstrates this idea in his description of his research on epigenetics: the study of how the activity of our genes can change, without changing our DNA sequences. He describes the genome as six billion letters of DNA that form words that are different in nature. When they are organized into sentences, each of them tells a unique story.

In order to form specific parts of our body, such as muscle and brain tissue, we organize our genome, represented here as letters, in different ways to create distinct sentences. The folding process is guided by epigenetic events, or post-it notes, which highlight the regions of our genome that need to be read.

Perhaps we can say that art relates in the same way. Each stroke of the brush or strike of the pen creates a unique image, and the artist goes over certain areas of the painting with these tools to highlight parts of the piece. Sometimes this disrupts the image, which can create chaos. Other times, this enhances the image with clarity.

Like epigenetics, one must follow these fine lines or broad strokes to understand how the larger image, or genome, has come to be. Lupien emphasizes that fostering creative thought can open a world of possibilities for all walks of life. “Bringing these values into your everyday practice as a researcher can serve to nourish your approach to work,” he said.

Experiencing art can also serve as time for our ideas to incubate, perhaps creating a period of unconscious processing for approaching problems in research. Taking from the famous 1929 works of Graham Wallas, The Art of Thought, incubation allows us to process problems in a manner whereby no direct effort is exerted.

We can optimize the way we process pre-existing knowledge by exposing ourselves to creative mediums such as art. This may lead to new approaches in scientific work. Ultimately, generating a scientific discourse with the expression of art can bring forth creative magic that inspires research. 

“In research, there are two things of value — there is knowledge and creativity,” said Lupien.

“You need to have balance. Never shy away from engaging in creative thought. You never know where it will take you.”

U of T student wins Pioneer Tournament with team for innovation that predicts human cancer risk

Hannah Le and teammates developed an innovation that blends AI, machine learning, and genomics

U of T student wins Pioneer Tournament with team for innovation that predicts human cancer risk

As many U of T students were wrapping up classes in March, first-year engineering student Hannah Le and her team won the third Pioneer Tournament — a worldwide competition that rewards participants for developing innovative ideas — for their project that used machine learning to identify and understand human biomarkers that predispose individuals to certain diseases.

Competition participants submit their project online and post weekly progress updates. The project then earns points awarded by contestants, who vote on the updates. After three weeks, the project becomes eligible to win a weekly prize, which is awarded to the team that wins the highest number of points at the end of that week. A project that places as a finalist for three weeks wins the team a larger award.

Le and her team members — Samarth Athreya, 16, and Ayaan Esmail, 14 — earned a top spot on the leaderboard in March and were awarded $7,000 from Pioneer to put toward their project. 

How the team got together

“Samarth, Ayaan and I met each other at an organization called The Knowledge Society in 2017,” wrote Le to The Varsity. The Knowledge Society is a startup incubator that exposes high school students to emerging technologies, such as artificial intelligence (AI), virtual reality, and brain-computer interfaces.

When the three innovators met, Esmail was working on a project that could accurately pinpoint and target cancer cells, while Athreya was working with machine learning models. With Le’s interest in genetics, the three decided to team up and investigate whether there was a way to use metabolic data to predict the onset of a disease.   

“I became incredibly curious on how we can decode the 3 billion letters [of DNA] in every cell of our body to increase human lifespan and healthspan,” wrote Le.

“Inspired by my grandmother who passed away due to cancer, I started asking myself the question: [could] there possibly be a way for us to predict the onset of cancer before it happens, instead of curing it?”

How Le’s team developed a model for predicting the risk of cancer development

At its core, the team’s AI platform uses a patient’s biological information to predict their risk of developing certain forms of cancer.

Metabolites are molecules that play a key role in maintaining cellular function, and some studies have shown that high levels of certain metabolites can signal the progression of lung cancer. But to develop and test their model, the team needed a large amount of metabolic data.

“To overcome such [a] limitation, we had the fortune to reach out to mentors such as the Head of Innovation at JLABS, [a Johnson & Johnson incubator], for further guidance and advice,” wrote Le. “As our team cultivates a stronger database, we would be able to produce more reliable results.”

“As teenagers we were far from experts [in] the field but we were really hungry to learn,” added Le.

As participants of the Pioneer Tournament, Le and her team received the opportunity to select a board of virtual advisors, who would provide guidance for their project.

“I recalled contacting Josh Tobin at OpenAI to ask him about the use of synthetic data in genomics research,” wrote Le. “[That enabled] us to understand both the strengths and weaknesses of such [an] approach, allowing us to pivot on what models to implement.”

The competition as a learning experience

Le remembers the Pioneer Tournament as an exciting chance to learn about different machine learning models and what made them effective as well as other projects that fellow participants were working on, all while attending courses at U of T.

“First year was an interesting journey of challenging course content, intertwined with unexpected personal growth,” wrote Le. “I learned how to strike a balance between working on personal projects, meeting interesting people, while completing my school work.”

And while Le is intrigued by the intersection of machine learning and genomics, she wrote, “I hope to keep an open mind and continue to be curious about the world around me.”

The genetic basis of oxygen-deprived tumours

PhD candidate Vinayak Bhandari studies genetic drivers of cancer

The genetic basis of oxygen-deprived tumours

A recent study published in Nature Genetics sought to determine the effects of hypoxia — low levels of molecular oxygen — on the development of cancer, including how it may speed up cancer growth. Lead author Vinayak Bhandari, a PhD candidate in U of T’s Faculty of Medicine and the Ontario Institute for Cancer Research, examined hypoxia in over 8,000 tumors across 19 tumour types.

Hypoxia can have detrimental health effects, one of which is that it can cause cancer cells to proliferate. 

According to Bhandari, normally, blood vessels in our bodies are well-organized and able to transport nutrients, including oxygen, to all cells. This changes in tumours.

“In tumours, the blood vessels are often very disorganized and have sluggish blood flow,” wrote Bhandari in an email to The Varsity. This leads to low-oxygen tumours. “Around half of all solid tumours end up with low levels of oxygen.”

Hypoxic conditions can accelerate the spread of aggressive cancer cells. In tumours, cancer cells exist with different sets of mutations. Some cancer cells will be susceptible to hypoxic environments due to their specific mutation, and these cells often do not survive. 

“But other cells that have a specific mutation may not be affected by low oxygen,” wrote Bhandari. “So you end up enriching the tumour for cells with that aggressive mutation that can survive an extreme environment and you get a more aggressive cancer.”

Despite the threat that hypoxia poses, it has previously been a challenge to study its effects due to the invasive and difficult process of measuring oxygen levels in tumours. 

To remedy this, Bhandari and his team created an innovative method for examining tumour hypoxia in more detail. 

“We used several mRNA signatures to computationally quantify tumour oxygen levels with existing patient data. We then used this hypoxia information and looked broadly at lots of different genomic features of tumours and found some really interesting links in several cancers,” wrote Bhandari. “We then dug deeper into prostate cancer where we have really good long term data for how patients respond to treatments and we looked further into interactions between hypoxia, changes in the DNA and also how tumours change over time.”

Dr. Paul Boutros — former Associate Professor at U of T’s Department of Medical Biophysics, now at the University of California, Los Angeles, and the supervisor for this study — added that hypoxia and its relevance to cancer growth is still not well understood, but that this research is a significant step. 

“I think other researchers are going to be able to take advantage of these data to explore a lot of new angles,” wrote Boutros. 

Boutros believes that other researchers will begin to look at genomics associated with hypoxic cancer cells, and begin to look more into genomic data in a new light. Boutros also adds that this research highlights how hypoxic environments arise due to different factors aside from genetic mutations, including cell morphology and evolutionary properties. 

Bhandari emphasized the multidisciplinary nature of the team involved in the research, and how it was an asset. 

“We were only able to do this because we had biologists, chemists, data scientists, statisticians, engineers, pathologists and radiation oncologists come together to work on this problem in asymmetric fashion. Everyone contributed in important ways over many years and I think this is the best way forward for answering difficult questions.”

A loophole in the cancer cell cycle is found

Researchers uncover an inhibitor that could halt cancer progression

A loophole in the cancer cell cycle is found

YAP and TAZ are proteins that have long been recognized for their role in regulating transcription — a process in which the information in DNA is copied into RNA — and are particularly relevant in cancer development.

A recent study in Nature Communications led by Mandeep K. Gill in U of T’s Department of Biochemistry identified NUAK2 as a gene that could control YAP/TAZ activity.

In normally functioning cells, YAP and TAZ are responsible for forming and regenerating tissues. In tumours, however, these proteins are able to initiate and metastasize, or spread, cancer cells to other parts of the body, as well as initiate the tumours.

“The relatively recent discovery (roughly 10 years) of the so called  ‘Hippo pathway’ which normally acts to limit excess cell growth and the demonstration that it is turned off in most cancers has provided a new target for the development of therapeutics,” explained Liliana Attisano, a principal investigator of the study also from the Department of Biochemistry, in an email to The Varsity.

The Hippo pathway is a process that controls tissue and organ development in mammals, especially in their size, by regulating cell growth and death, and controls the transcriptional activity of YAP and TAZ proteins.

The pathway can be activated by various factors, after which it engages its core cassette — a subunit made of enzymes known as kinases, which are involved in the movement of phosphate groups, or phosphorylation.

When a cascade of phosphorylation — the addition of a phosphate group — occurs in the cassette, YAP and TAZ are marked with phosphate groups and are targeted for degradation.

When the Hippo pathway is inactive, however, YAP and TAZ accumulate in the nucleus and latch on to the DNA-binding proteins in there, which can lead to cancer cell proliferation. 

Attisano and her team discovered NUAK2 was found to encode a protein that results in even more YAP and TAZ getting into the cell’s nucleus to further promote abnormal cell growth.

The researchers started by conducting studies in breast cancer cells and were able to identify  the kinase NUAK2 as a positive regulator of YAP and TAZ activity.

According to the study, “NUAK2 functions in a kinase-dependent manner to promote nuclear YAP/TAZ localization and activity” and promotes YAP and TAZ activity in a positive feedback loop.

A decrease in NUAK2 is therefore found to reduce transcriptional activity and the quantity of YAP and TAZ in the nucleus. As well, kinase-deficient NUAK2 was found to restore YAP and TAZ localization in the nucleus, which deemed NUAK2 an activator of YAP and TAZ activity.

“We found a way to restore the activity of the pathway (by removing or blocking NUAK2 activity),” wrote Attisano.

A lack of NAUK2 in cells showed a reduced cell growth and robust tumour growth in mice.

Tests were conducted on bladder cancer cells to determine the implications for human tumour progression. Larger increases of NUAK2 were found in high-grade samples that came from patients who had experienced a relapse.

These findings could be applied to cancer treatments as blocking the expression of or inhibiting NUAK2, YAP, and TAZ appears to restore Hippo pathway activity and cell growth, thus limiting tumour progression.

“There is still a long road ahead,” wrote Attisano. “But the next step would be [to] develop specific and potent compounds that can be tested in mouse and human organoid models with the long-term goal of… identifying a drug that can be used in patients.”

U of T prof’s startup takes cancer therapy to clinical trials

Pionyr Immunotherapeutics raises $62 million in series B investment round

U of T prof’s startup takes cancer therapy to clinical trials

A biotech startup co-founded by Sachdev Sidhu, a professor in U of T’s Department of Molecular Genetics, has drawn in $62 million USD following a second round of funding, bringing its total investments to $72 million USD.

Pionyr Immunotherapeutics, which is now planning to take its anti-cancer therapy to clinical trials, initially began as a research collaboration between Sidhu and Max Krummel, a professor at the University of California, San Francisco School of Medicine. Founded in 2015, the California-based startup combined Sidhu’s expertise in antibody phage-display technology with Krummel’s immune system biology research.

This project is a collaborative effort with Toronto Recombinant Antibody Centre (TRAC), which was founded by Sidhu and Dr. Jason Moffat, who is also a Molecular Genetics professor at U of T. Housed in the Donnelly Centre for Cellular and Biomolecular Research, TRAC researchers are working to harness the therapeutic potential of synthetic antibodies.

Synthetic antibodies can be engineered to target a variety of molecules implicated in disease and they are key for drug development. Pionyr’s anti-cancer therapy, known as Myeloid Tuning, uses the high specificity afforded by synthetic antibodies to bolster the immune system’s defence against cancer by manipulating a tumour’s microenvironment.

The immune system uses T cells to detect foreign molecules to evoke a defensive response. Because tumours are created from existing cells in the body, they evade recognition by T cells, dampen the immune response, and proliferate uncontrollably. The key is to restore the body’s immune capacity to fight cancer — this is the premise of immunotherapy in oncology, better known as immuno-oncology.

“So the idea there is simple: you want to turn on a T cell, you simply find proteins that are inhibiting that T cell,” said Sidhu.

Myeloid Tuning achieves this by “alter the tumour microenvironment to favour immune-activating cells over immune-suppressing cells” and enhances anti-tumour defenses. “T cells are activated not by targeting them but by eliminating the inhibitory cell population,” said Sidhu.

Pionyr’s technology could also complement existing anti-tumour therapies like T cell checkpoint inhibitors. Checkpoints are regulators that mediate communication between T cells and the immune system. They are responsible for fine-tuning the body’s immunity and downregulating it when it detects native cells, which would otherwise lead to an autoimmune response. By incorporating checkpoint inhibitors, therapies can be developed to block a tumour’s ability to evade T cell detection.

Ipilimumab, commercially known as Yervoy, set the precedent by becoming the first United States Food and Drug Administration-approved therapeutic antibody against skin cancers and for ushering in a new wave of immuno-oncology. The drug, co-invented by Krummel, inhibits cytotoxic T-lymphocyte-associated protein-4, one of many checkpoints found on T cells. Similarly, pembrolizumab, or Keytruda, inhibits the checkpoint called programmed cell death protein 1 (PD-1).

“Anti-PD-1 binds the T cell and… activates it that way, and then we add another antibody that eliminates inhibitory myeloid cells, so you get double [the effect],” said Sidhu.

Sidhu says there is a critical question in field: does the rest of the tumour simply not have T cells that can attack them or are there additional yet unidentified breaks? These possibilities are not mutually exclusive and are already being investigated. According to Sidhu, the future of immuno-oncology is already here.

Myeloid Tuning is a very promising method, but it is not the only immuno-oncology treatment in the works. Currently, therapeutic agents being researched involve other immune cells like macrophages and natural killer cells that can be exploited for anti-tumour therapies.

“[There is] very little that is not being explored as far as immune cell activation,” said Sidhu. “It’s exciting in that, while only a subset of cancers responds to immunotherapy, the ones that do respond often respond tremendously.”

National Cancer Institute invests $4 million in Pathcore

U of T based start-up leverages the power of computation to transform pathology

National Cancer Institute invests $4 million in Pathcore

Quick and accurate diagnosis is vital to effective treatment, anything that can make pathology more efficient might be a literal life-saver.

Pathcore, a start-up based at the University of Toronto’s Impact Centre, aids this process by employing the power of computerized quantitative methods to transform the field of pathology. Using algorithm-based image analysis, the start-up helps pathologists make diagnoses more accurately and more efficiently.

“Pathology is a very analogue field that still relies on microscopes and human interpretation to diagnose complex diseases,” says Dan Hosseinzadeh, CEO and co-founder of the start-up. “We feel that computers can assist the pathologists in certain routine, time consuming, and tedious tasks, thereby allowing the human pathologists to focus on the complex decision-making by synthesizing information from various sources into a diagnosis.”

The Sedeen Viewer, is one of Pathcore’s products that allows pathologists to annotate and analyze whole slide scans of tissue samples. Pathologists can then apply tissue- and disease-specific algorithms to the images to make clinical diagnoses.

Sean Nichols, Pathcore’s Lead Web Developer explains that, “for prostate cancer, you might have an algorithm that calculates what’s called the Gleason score, which is a scoring method for grading the aggressiveness of prostate cancer. In that case you might look across the whole image or select a few areas that are representative, and then run the algorithm on it.”

Pathcore has also developed assisted algorithms that automate repetitive tasks such as cell counting. “So right now pathologists would look at an area and say there’s about 200 cells, whereas an algorithm could tell you exactly how many it detects,” says Nichols.

“The main challenge is coping with the vast amount of information available when specimens are imaged at high resolution… Also understanding the complex nature of the disease process is challenging and important for building good algorithms,” says Hosseinzadeh.

Pathcore’s technology is currently being used by over 100 organizations around the world. The $4 million (CAD) investment from the US’ National Cancer Institute will accelerate algorithm development for cancer detection. This investment will allow the company to expand its Software Development Kit to support its partner institutions as they build their own algorithms.

Additionally, the company is “hoping to improve on the usability of the [Sedeen Viewer] and potentially hire some more developers to improve the software,” says Deyu Wang, product designer at Pathcore.

The start-up is a spin-off from a research project originally supported by the Ontario Institute for Cancer Research and the Sunnybrook Research Institute.

The Impact Centre nurtures early stage start-ups by providing a range of services, including marketing, consulting, and legal support. It also provides a physical space for start-ups at little or no cost. Nichols explains that the Impact Centre “puts all these start-ups in an environment together to kind of interact with each other and give each other advice.”

U of T students interested in working at a start-up should enroll in IMC200 (Innovation and Entrepreneurship) and IMC390 (Internships in New Ventures). The latter allows students to complete a placement at an Impact Centre Company.

The three characteristics of a successful start-up, Hosseinzadeh argues are, “a dedicated and hardworking team, a niche product, [and] a strong network.”

U of T-based cancer research group hailed as ‘Dream Team’

Dr. Peter Dirks and colleagues receive $11.7 million to lead new cancer stem cell research initiative

U of T-based cancer research group hailed as ‘Dream Team’

In 1961, Toronto researchers verified the existence of stem cells. Now, in 2016, a Canadian ‘Dream Team’ of researchers assembles to tackle cancer stem cells.

Announced on World Cancer Day, Dr. Peter Dirks, a neurosurgeon at the Hospital for Sick Children and a professor in the departments of surgery and molecular genetics at the University of Toronto, will lead this $11.7 million initiative funded by Stand Up to Cancer (SU2C), among other organizations.

Co-led by Dr. Samuel Weiss, director of the Hotchkiss Brain Institute at the University of Calgary, the team brings together scientists across Canada in a collaborative approach to make a difference for children and adults with brain cancer.

“The [goal of this] project is to understand brain cancer from a cancer stem cell perspective,” says Dr. Gary Bader, a Dream Team principal investigator of the Donnelly Centre for Cellular and Biomolecular Research. “The best treatments [currently] are not very effective. They do extend your life by…a few months.”

The Dream Team is dedicated to translational research, which aims to move discoveries from the lab and implement them in medical practices by bringing new treatments for brain cancer into clinical trials.

The primary targets are cancers known as glioblastomas and ependymomas, both of which are types of brain tumours. Less than 10 per cent of adults with glioblastoma survive for five years after diagnosis, and brain tumours are now the leading cause of death in children with cancer.

When healthy, stem cells in the brain will develop into normal nerve cells. Certain stem cells with deleterious changes, on the other hand, can become cancerous. These cancerous stem cells can regenerate tumours even after surgery and therapy. Many cancerous stem cells will resist drug treatments as well.

The researchers intend to approach this challenge in three ways: first they will conduct a detailed analysis of brain tumour stem cells to better understand the biological profile of these cells. Then, they will explore new drug combinations through a careful screening of chemicals. Finally, the team will test five promising drugs in clinical trials that may potentially be the solution to glioblastomas and ependymomas.

Dr. Amy Caudy, a professor in the department of molecular genetics and Canada Research Chair in Metabolics for Functional Enzyme Discovery, is a Dream Team principal investigator. As part of the interdisciplinary approach against brain cancer, her team is investigating the links between cancer cells and metabolism, specifically a metabolite (a chemical produced in the body during digestion) called 2-hydroxyglutarate (2HG).

“[2-HG is] very central to the pathogenesis of at least some of these glioblastomas,” says Dr. Caudy, emphasizing the disease-triggering abilities of 2-HG.  “People are now using it as a biomarker for [the] progression and status of glioblastomas and also some other cancers.”

With project leaders Dr. Dirks, who first discovered brain cancer stem cells, and Dr. Weiss, who received the Canada Gairdner International Award for discovering adult neural stem cells, the team of fourteen researchers stand up to cancer. Together, the Dream Team continues Canada’s legacy in stem cell research.

From Varsity Blue to philanthropist

Stephanie Rudnick’s Swish for the Cure event has raised thousands for childhood cancer research

From Varsity Blue to philanthropist

Stephanie Rudnick is a former Varsity Blues basketball player who played for current U of T head coach Michele Belanger during the 1994-1999 seasons. In 1999, Rudnick was intent upon playing out her final year of eligibility wearing blue and white. She had goals to “win a National Championship, become an OUA All Star, an All Canadian, and then play pro in Israel.” Following these achievements, Rudnick planned to return to Canada and start her own basketball camp. 

Playing through several back injuries, Rudnick was named an OUA All Star in her fourth year. Before being able to check another goal off her list, Rudnick’s life took an unexpected turn. In May 1999, her father was diagnosed with stage four cancer, and passed away only two months after his diagnosis. Devastated and injured, Rudnick did not return to the Blues that fall and was forced to revise a plan that she had dedicated years of her life to fulfilling.

No pro contract, no business education, and in the midst of a devastating loss, Rudnick was left without direction. “Feeling self-defeated I cried to him about how my old plan was ruined,” Rudnick explained how she reacted when a friend asked about what she would do next.

It was only after this meeting and some serious thought that Rudnick conceptualized Elite Camps. Born out of pain, Elite Camps is one of the largest and longest running basketball organizations in Canada. Based in the GTA, Elite Camps sees more then 3,000 kids every year and is in its seventeenth year of operation.

To avoid competition with rival clubs, Rudnick explains that her first camp was launched over the holidays: “I found out that Passover was a time with no programming. I decided I would try to run my first camp at that time [to avoid competing with other camps in the GTA].”

Rudnick pursued mentorship from another camp director, joined the Ontario Camping Association, and reached out to her former Varsity Blues teammates to work at her camp. What started as one camp in Toronto soon grew into two, and now Elite Camps runs over 37 sessions in multiple cities.

Next came Swish for the Cure. “A few years after I started my business I really wanted to do something to honour [my father’s] memory,” Rudnick explained, which is how Swish for the Cure — celebrating its tenth anniversary on February 6, started. Swish for the Cure has raised over $135,000 to date for in the name of the Childhood Cancer Foundation. Rudnick explained that the event has evolved in the past ten years from a way to raise money for cancer research, to an opportunity to provide families of children with fighting cancer “a free day of fun, food and time with their family in a safe environment…[including] basketball activities, arts and crafts, carnival activities and many popular local child entertainers.” 

At the time of the first Swish for the Cure, Elite Camps was not the expansive chain of basketball camps that it is today. While Rudnick isn’t one to consider herself a philanthropist out of modesty, she would concede that philanthropy is a lot like playing basketball. Effective philanthropy fills a void in society in the same way that an effective player meets the needs of their team. It can be something small, like rebounding, or something more pronounced like accepting a leadership role.