Digital Biology and the Deep Blue Sea

"Digital biology," as I use the phrase, refers to the idea of using digital information for doing biology. This digital information comes from multiple sources such as DNA sequences, protein sequences, DNA hybridization, molecular structures, analytical chemistry, biomarkers, images, GIS, and more. We obtain this information either from experiments or from a wide variety of databases and we work with this information using several kinds of bioinformatics tools.

The reason I'm calling this field "digital biology" and not "bioinformatics" (even though I typically use the terms as synonyms) is that many people assume that using bioinformatics requires programming, and there are fewer assumptions about the requirements for doing digital biology. Digital biology does require using software, it does not require learning how to program.


Recently, The Reef Tank interviewed me to learn what digital biology can tell us about the ocean.

The questions are from the Reef Tank.  The answers are mine.

1.It sounds like you've had many different jobs. Tell me about what you've done in the past and how you eventually found your calling (if you believe digital biology is your true calling.)

It does sound that way, but all the things I've done have been tied together by my love of biology and interest in finding new ways to explore the living world. In some respects, the ability to do the kind of research I do, came to me with the development of the Internet. I don't have a lab, so I need an alternative. Fortunately, the availability of digital tools and resources has allowed me to connect with biology and data from all over the world.

2.Explain digital biology and the different ways it can be used.

The phrase "Digital Biology" comes from a conference I attended at the National Institutes of Health in 2003. The NIH, of course, is focused on human health, and was primarily interested in the advances in computational tools would impact biomedicine. Digital Biology however covers much more ground than human health. It includes all the ways we use digital resources to learn about the living world, from the sequences of nucleic acids to natural products to the relationships between all living things through evolution.

3.How can digital biology be used in a marine biology sense?

There are many examples of this. Digital biology can help us in categorizing living organisms and understanding how they're related. Much of this information can be found in taxonomy databases. We can use mapping technology to see where sea creatures live and where they migrate.

I know fish and wildlife officers and the FDA have used DNA sequencing to identify the source of different fish.

I think one of the best examples of digital biology in marine research comes from Dr. Craig Venter's work, sailing around the world and sequencing the nucleic acids in the oceans. His Sorcerer II Global Ocean Sampling (GOS) expedition yielded 6.2 million predicted protein sequences. He found new biochemical pathways and hundreds of new viruses. His work is an example of digital biology technique, called "metagenomics," where researchers interrogate the environment through DNA sequencing. This work is leading to many new discoveries and mechanisms for understanding our world.

4.Have you done any exploring in marine biology/marine life using digital biology? What have you found?

Last fall, I taught a bioinformatics class where our whole college got involved in an environmental sequencing project. Our technician collected the samples from a local creek. The microbiology class grew colonies of bacteria from the samples on agar plates. The biology class isolated and amplified DNA. The biotech class sequenced the DNA. And our class analyzed the sequences and counted the different kinds of microbes that were found. Ideally, we would like to know whether the composition of microbes changes from year to year and how the number and kinds of microbes is related to the health of the stream.

5.What does it tell you about marine biology that perhaps another form of research wouldn't?

Well, sequencing DNA allows us to study microbes that we can't culture. The information that we get from metagenomics kinds of studies tells us about life that we can't see.

6.Do you think it's possible that problems that affect the marine life world (pollution, ocean acidification, climate change, global warming) could potentially be solved using digital biology?

Digital biology can't solve problems. We need humans to do that. What digital biology can do is give us a way to measure changes and help us make connections between our actions and the results. If we do something that improves the health of an ecosystem, for example, our digital tools could help us measure those improvements. In the same respect, we could also find out we've made changes the cause more damage.

For example, there is a controversy in Washington State right now about shellfish farming. The people living along the Puget Sound claim that shellfish farming hurts the environment. The geoduck farmers claim that the opposite is true, that shellfish help clean the environment. Biology gives us a way to find out which story is correct.

7.Do you think people are more generally aware of the issues that affect marine life thanks to digital biology?

It's possible that Craig Venter's trips have helped raise awareness of the oceans' plight, but I don't know if don't if that's really true.

8.How could digital biology help a marine scientist or marine biologist?

There are many, many ways.

Let's say marine biologist finds a fish and they want to know if it's a new kind of fish. They could sequence some of the fish DNA and figure out if it's a new fish and how it's related to other fish.

There is also a protein from a jellyfish, called "Green fluorescent
protein," that has become very important for all kinds of biological
research. One of the researchers who studies this protein, Roger Tsien,
won a Nobel Prize last year because his work with GFP has been so
important to biological research.

Imagine a biotech company wants to understand how a barnacle attaches to a rock. With the genome sequence of a barnacle, they could find the biochemical pathways and figure out which ones are unique. The proteins that would be predicted from the genome sequence would give them insights about the enzymes that produce barnacle glue.
Researchers are also very interested in the travel of microbes through the oceans and the potential for cruise ships to carry human viruses and pathogenic bacteria. Environmental sequencing could provide the tools to help us monitor contamination and environmental change.

9.Could it help a reef hobbyist who just has a hobby of taking care of his/her aquarium?

I could see a hobbyist using digital biology in at least two ways. First, a hobbyist might search on-line databases to learn more about their favorite species and gain knowledge about the proper techniques to care for those species. Second, a time might come when a hobbyist could take a sample from their aquarium, send to a lab for DNA sequencing, and get a result about the health of the environment in that aquarium. This test might detect pathogens or some kind of imbalance in the microbial community. It might be a long time though, before this test is affordable.

There is another way that hobbyists benefit. Hobbyists can buy genetically modified zebra fish at Walmart. GloFish are quite lovely and a great example of using digital biology and biotechnology to make something pleasant.


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