Templeton Foundation funds a grant on transposons

The John Templeton Foundation supports "interdisciplinary research and catalyze conversations that enable people to pursue lives of meaning and purpose." Many of these projects have religious themes or religious implications. The foundation is well-known for its support of projects that promote the compatibility of science and religion. You can see a list of recent grants here.

Templeton recently awarded a grant of $607,686 (US) to study the role of transposons in the human genome. The project leader is Stefan Linquist, a philosopher from the University of Guelph (Guelph, Ontario, Canada). Stefan has published a number of papers on junk DNA and he promotes the definition of functional DNA as DNA that is subject to purifying selection [The function wars are over]. Other members of the team include Ryan Gregory and Ford Doolittle who are prominent supporters of junk DNA.

Here's the description of the grant.

Transposable genetic elements as ecological agents

The genome is typically regarded as an instruction manual for building an organism. However, the majority of DNA in every plant and animal cell derives from the activity of transposable elements (TEs) or “jumping genes.” These entities exploit the cell’s replication machinery to self-copy and reinsert into new chromosomal locations. TEs have long been recognized as evolutionary agents in the (minimal) sense of behaving like genomic parasites: they initiate and control their own replication in ways that benefit their populations, sometimes at the expense of the host organism.

Our project is distinctive in regarding TEs also as ecological agents. This involves identifying specific features of a genome (e.g. chromosome structure, gene density, methylation patterns) that impact the abundance, distribution, and diversity of TE populations. Put differently, our project regards individual TEs as if they were organisms residing within an intra-cellular ecosystem. By identifying a variety of niches and ecological interactions within genomes, this new perspective will transcend the simplistic dichotomy between functional versus “junk” DNA. It will also shed light on otherwise perplexing questions about variability in genome size, such as why the genome of an onion is five times larger than that of a human.

This project will generate 15-20 articles clarifying foundational concepts and applying ecological methods to genomic data. Our project includes interdisciplinary training for two postdocs and several graduate student researchers. We will also host two “hothouse” workshops on genome-level ecology, where early career researchers from different disciplines collaborate on small projects. The primary outcome of this project will be the establishment of genome-level ecology as a novel and exciting discipline. By harnessing insights and methods from the science of ecology we will shed new light on the structure and function of DNA.

I interpret this to mean that the group will only study active transposons; that is, transposons that are still capable of moving around in the genome. This is important because most of the junk DNA in our genome is derived from ancient transposons that have been rendered non-functional by mutations, including insertions and deletions.

It's difficult to determine the exact amount of the human genome that's related to transposons because over time the sequences acquire so may mutations that their history is obscured. There is widespread consensus that at least 50% of the human genome contains transposon-related sequences and some estimates run as high as two-thirds of the genome (de Koning et al., 2011). There appear to be about 20 active transposons in the human genome. Most of them are members of various Alu families and the most abundant is the LINE-1 Hs element. The active transposons make up about 0.05% of the genome (Milles et al., 2007; Konkel et al., 2015; Aution et al., 2012).

Linquist and his collaborators are interested in the old idea of transposons as examples of selfish DNA. That's not a controversial issue as long as you recognize that it only refers to active transposons and should not be confused with Dawkins' selfish genes [see: Selfish genes and transposons; Junk DNA and selfish DNA]. This has very little to do with junk DNA except for the fact that selfish transposons are the original source of most junk DNA.

Active transposons are functional in the sense that they are capable of transposition and some of them encode active enzymes such as transposase. Linquist and his collaborators make a distinction between functional transposons and other functional regions of the genome. The distinction is based on levels of selection. Junk DNA is DNA that's not required for the survival of the organism so by this definition active transposons are junk. They are only functional a lower level of organization; namely, the genome [The Function Wars: Part II].

The purpose of the grant seems to be to examine the role of active transposons (selfish DNA) within genomes by treating the genome as the "ecology" in which active transposons operate. The authors employ the buzzwords "agent" and "agency" to describe active transposons and their actions. I'm pretty sure they know why Templeton would be sympathetic to the idea of agency and purpose.

Now let's look at the University of Guelph press release published a few days ago (April 10, 2025).

One Person’s Junk: U of G Researcher Explores Alternative Approach to Understanding DNA

A philosophy professor at the University of Guelph is leading a team of biologists to examine a theory that might change the way we view parts of our genetic makeup.

Dr. Stefan Linquist, professor in the Department of Philosophy, College of Arts, will receive $836,711 from the John Templeton Foundation to investigate the functions of transposable elements (TEs), or “jumping genes,” and their relationship to the organisms they’re found within, including us.

“Being a philosopher and the lead investigator on a study about molecular biology – it’s not something you see every day,” says Linquist. “But philosophy is about asking big questions to gain a better understanding of the world, and there are some big puzzles in the genome that have yet to be solved. I think one of them is this concept of function as it relates to our DNA.”

In this project, Linquist’s big question asks us to look at these elements from an ecological perspective.

What if TEs, instead of functioning for the organisms they’re found within, are acting out of their own biological self-interest? What if they’re more like organisms themselves with their own agendas?

I don't think this is controversial. We've known for 45 years that transposons are examples of selfish DNA.

Questioning the functional vs. junk DNA dichotomy

Linquist says that most DNA in plant and animal cells consists of TEs, and in humans, they make up between 40 and 60 per cent of our genome. But their significance to us has been the subject of a longstanding debate among scientists.

“For the past 50 years, scientists have operated with a fairly simplistic dichotomy, classifying all DNA as either functional or junk,” says Linquist. “To be considered functional means that a strand of DNA somehow contributes to the development or maintenance of the organism as a whole – whether that’s coding for proteins or switching other genes ‘on’ and ‘off.’ If it doesn’t do either of those things, then historically, it was considered junk.”

Let's ignore the fact that there's more to function than just protein coding and regulation. If DNA is subject to purifying selection then it's functional and if it's not then it's junk. Purifying selection operates at the level of the organism within a population. Transposons are not subject to purifying selection at this level and that's why our genome is chock full of degenerate transposon-related sequences. They are junk by the definition that Linquist and his collaborators have used in the past.

TEs are a type of non-coding DNA. Similarly to viruses, they use a cell’s DNA replication machinery to make copies of themselves that gradually spread throughout a genome, “jumping” from their original locations and landing elsewhere.

Depending on where they reinsert themselves, TEs can have negative effects on neighbouring genes.

At the same time, they are seen as contributors to genetic diversity and evolution by rearranging parts of our internal code and will occasionally become “domesticated” – meaning their sequences are hijacked by the rest of the genome to perform functions that benefit the organism.

All of this raises the question: how should TEs be classified?

Linquist believes the current distinction is too binary for this type of DNA and has led some to exaggerate how useful TEs may be for the organism.

“Scientists recognize that TEs are biochemically significant, and since they don’t fit neatly into the ‘junk’ bin, there is a tendency to assume their purpose is beneficial,” he says. “But they can still be performing biological actions without directly contributing to the development or maintenance of the organism.”

There's nothing new here. The scientific literature is full of papers discussing transposons as selfish DNA and documenting the fact that some transposon-related sequences have been co-opted to become functional at the organism level.

Many scientists have claimed that most of our genome is functional and that includes most of the transposon-related sequences. Those scientists aren't referring to the active transposons (0.05% of the genome) that Linquist et al. are studying. The anti-junk scientists aren't confused about whether active transposons fit neatly into the "junk" bin—they are confused about the definition of function at the organism level.

Ecological approach to DNA science

Linquist and his team, including Drs. Karl Cottenie and Ryan Gregory, professors in the Department of Integrative Biology, College of Biological Science; Dr. Stefan Kremer, professor in the School of Computer Science, College of Physical and Engineering Sciences; PhD graduates Drs. Tyler A. Elliott and Brent Saylor and Dr. W. Ford Doolittle, professor emeritus at Dalhousie University, are taking an ecological approach to understanding TEs.

“The science of ecology has a rich vocabulary to describe roles a species might play within a broader ecosystem,” says Linquist. “Some ecological interactions promote the survival of one species while excluding others. Some are mutualistic, in which two or more species benefit each other, and others benefit the ecosystem at large.”

According to Linquist, this provides a clue for reconceptualizing TEs. He says, with some imaginative reframing, TEs can be viewed as ecological agents whose activities can affect the structure, function and dynamics of their environment. It could also explain why TEs from different “families” will reinsert themselves in specific regions of a chromosome as if they are selective about where they land, and why their population numbers vary among genomes.

The project team will analyze genomic data using ecological tools, construct computer simulations of TE behaviour and explore the conceptual foundations of genomics and ecology, outlining what it means to think of the genome as a literal ecosystem and the implications for biomedical science.

Linquist thinks this approach could revolutionize the study of genomics by creating new categories for classifying DNA and paving the way for more research in this area.

“The work that Dr. Linquist and his team are doing has the potential to break even more ground in an emerging, multidisciplinary field,” says Dr. Shayan Sharif, interim vice-president, research and innovation. “Research excellence is about pushing boundaries and expanding the frontiers of our knowledge. This funding from the John Templeton Foundation will propel this exploration forward and support Dr. Linquist and his team in their pursuit of new discoveries.”

It will be interesting to see whether the work really does revolutionize the study of genomics.

Call me skeptical.

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Autio, M.I., Bin Amin, T., Perrin, A., Wong, J.Y., Foo, R.S.-Y. and Prabhakar, S. (2021) Transposable elements that have recently been mobile in the human genome. BMC Genomics 22:1-17. doi: 10.1186/s12864-021-08085-0

de Koning, A., Gu, W., Castoe, T.A., Batzer, M.A. and Pollock, D.D. (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7:e1002384. doi: 10.1371/journal.pgen.1002384

Konkel, M.K., Walker, J.A., Hotard, A.B., Ranck, M.C., Fontenot, C.C., Storer, J., Stewart, C., Marth, G.T., Consortium, G. and Batzer, M.A. (2015) Sequence analysis and characterization of active human Alu subfamilies based on the 1000 genomes pilot project. Genome Biology and Evolution 7:2608-2622. doi: 10.1093/gbe/evv167

Mills, R.E., Bennett, E.A., Iskow, R.C. and Devine, S.E. (2007) Which transposable elements are active in the human genome? TRENDS in Genetics 23:183-191. doi: 10.1016/j.tig.2007.02.006