Menus Subscribe Search

Follow us


Genes Are Us

biology

(Photo: mystel/Shutterstock)

It Doesn’t Matter That Not Everything Matters

• March 14, 2014 • 12:00 PM

(Photo: mystel/Shutterstock)

Why scientists need to stop worrying about whether or not everything in biology serves a purpose.

John Brockman, the publisher and science impresario who runs the online science and culture salon Edge.org, has asked his provocative, annual Edge question: What scientific idea is ready for retirement? “Few truly new ideas are developed without abandoning old ones first,” Brockman writes. “What established scientific idea is ready to be moved aside so that science can advance?”

Here’s my candidate for forced retirement: The idea that we need to distinguish between things in biology that are there for a purpose and those that aren’t.

Because purpose is such a distinctive feature of life, discovering the functions of individual biological parts has been a major goal of life scientists for over 2,000 years. Aristotle made it a part of his scientific agenda. Galen, physician to Roman Emperor Marcus Aurelius in the second century, argued that nature had shown “forethought and art” in the design of animals’ bodies and thus the only way to fully understand an organism was to discover the purpose of each of its parts. Nearly 1,500 years later, William Harvey, who discovered the function of the heart, argued that “Nature, perfect and divine, making nothing in vain,” does not add unnecessary components to living things. Galen and Harvey ascribed biology’s exquisite functional designs to a Designer. When Charles Darwin and Alfred Wallace discovered evolution by natural selection, they got rid of the Designer but not the design.

There is no reason our DNA can’t be a mixture of the absolutely functional, the non-functional, and the sort-of functional.

Over the last century, biology has gone molecular, and the modern-day search for purpose in biology has focused on assigning functions to the cellular components that lie at the intersection of life and non-life, particularly the DNA, RNA, and protein molecules that do the major jobs of the cell. But when you get down to the nanoscale level of molecular biology, the idea that each biological part has a definite function starts to become non-functional.

The most obvious place to see this is that we have too much DNA. Only about two percent of our DNA contains the instructions necessary for making the cell’s protein components. For decades, biologists have scratched their heads over the rest. What is its function? Is most of our genome a genetic wasteland? And humans aren’t the most genetically overloaded species: Amoebas, lungfish, salamanders, and onions have a lot more DNA than we do. In an influential 1980 paper, Ford Doolittle and Carmen Sapienza argued on evolutionary grounds that our genomes likely contain DNA that was of absolutely no use to us—”whose only ‘function’ is self-preservation.” Trying to assign a biological purpose to this DNA would prove to be “ultimately futile.”

Now that the study of DNA has become more central to biological science than ever before, the issue of how to distinguish functional from non-functional DNA has become a major point of contention. Because evolution is the driving force that creates function in biology, scientists frequently identify functional genetic elements by looking for DNA that is protected by evolution from function-destroying mutational erosion. Evolutionary conservation has been a crucial standard of evidence for determining whether a segment of DNA has a purpose.

But not everyone agrees with this standard. In 2012, the ENCODE project, a consortium of scientists tasked by the National Institutes of Health to make a comprehensive catalog of all of the functional DNA elements in our genome, published their results and claimed that, contrary to what scientists believed for decades, most of our DNA does in fact have a purpose: 80 percent of our genome is functional. (Full disclosure: Some of my research is funded by ENCODE.)

ENCODE’s sensational claim was widely covered by the press as a major scientific breakthrough, but it drew harsh responses from the scientific community. The heart of the dispute was over ENCODE’s definition of function. They abandoned the evolutionary standard and relied instead on finding DNA that carried certain biochemical features that are known to occur with functional DNA. University of Houston biochemist Dan Graur and his colleagues argued that ENCODE, by defining function in this way committed the logical fallacy of affirming the consequent—it may be true that all swans are white birds, but it’s wrong to conclude that every white bird is a swan. Graur accused the ENCODE scientists of seeing swans everywhere. Just because a functional piece of DNA has a particular biochemical feature does not mean that all DNA elements with that feature are functional. The only way to avoid this problem, Graur argued, is to stick with the evolutionary standard.

On the other hand, the ENCODE results showed that, functional or not, most of our genome is biochemically active. Things happen in the cell, whether they have a purpose or not. Biologists are discovering how evolution can build complex networks of interacting genes into our genomes for no particular purpose. The functional parts of our genome are embedded in a context of purposeless genetic junk that is nevertheless not inert, and it has the potential to cause serious problems when perturbed. Evolution is ultimately a probabilistic and continuous process; new function in the genome can arise from non-functional elements, and there is no reason our DNA can’t be a mixture of the absolutely functional, the non-functional, and the sort-of functional.

Ford Doolittle, at Dalhousie University in Nova Scotia, agreed with Graur that ENCODE went too far, but he also pointed out that the argument wasn’t so much about biology as it was about words: “there is no experimentally ascertainable truth of these definitional matters other than the truth that many of the most heated arguments in biology are not about facts at all but rather about the words that we use to describe what we think the facts might be.”

Doolittle is right, and biologists, of all people, should recognize that nature doesn’t fit into the neat categories that we define. What’s true of life in general is true of molecular biology as well: Not everything happens for a purpose.

Michael White
Michael White is a systems biologist at the Department of Genetics and the Center for Genome Sciences and Systems Biology at the Washington University School of Medicine in St. Louis, where he studies how DNA encodes information for gene regulation. He co-founded the online science pub The Finch and Pea. Follow him on Twitter @genologos.

More From Michael White

A weekly roundup of the best of Pacific Standard and PSmag.com, delivered straight to your inbox.

Recent Posts

November 25 • 4:00 PM

Is the Federal Reserve Bank of New York Doing Enough to Monitor Wall Street?

Bank President William Dudley says supervision is stronger than ever, but Democratic senators are unconvinced: “You need to fix it, Mr. Dudley, or we need to get someone who will.”


November 25 • 3:30 PM

Cultural Activities Help Seniors Retain Health Literacy

New research finds a link between the ability to process health-related information and regular attendance at movies, plays, and concerts.


November 25 • 12:00 PM

Why Did Doctors Stop Giving Women Orgasms?

You can thank the rise of the vibrator for that, according to technology historian Rachel Maines.


November 25 • 10:08 AM

Geography, Race, and LOLs

The online lexicon spreads through racial and ethnic groups as much as it does through geography and other traditional linguistic measures.


November 25 • 10:00 AM

If It’s Yellow, Seriously, Let It Mellow

If you actually care about water and the future of the species, you’ll think twice about flushing.


November 25 • 8:00 AM

Sometimes You Should Just Say No to Surgery

The introduction of national thyroid cancer screening in South Korea led to a 15-fold increase in diagnoses and a corresponding explosion of operations—but no difference in mortality rates. This is a prime example of over-diagnosis that’s contributing to bloated health care costs.



November 25 • 6:00 AM

The Long War Between Highbrow and Lowbrow

Despise The Avengers? Loathe the snobs who despise The Avengers? You’re not the first.


November 25 • 4:00 AM

Are Women More Open to Sex Than They Admit?

New research questions the conventional wisdom that men overestimate women’s level of sexual interest in them.


November 25 • 2:00 AM

The Geography of Innovation, or, Why Almost All Japanese People Hate Root Beer

Innovation is not a product of population density, but of something else entirely.


November 24 • 4:00 PM

Federal Reserve Announces Sweeping Review of Its Big Bank Oversight

The Federal Reserve Board wants to look at whether the views of examiners are being heard by higher-ups.



November 24 • 2:00 PM

That Catcalling Video Is a Reminder of Why Research Methods Are So Important

If your methods aren’t sound then neither are your findings.


November 24 • 12:00 PM

Yes, Republicans Can Still Win the White House

If the economy in 2016 is where it was in 2012 or better, Democrats will likely retain the White House. If not, well….


November 24 • 11:36 AM

Feeling—Not Being—Wealthy Cuts Support for Economic Redistribution

A new study suggests it’s relative wealth that leads people to oppose taxing the rich and giving to the poor.


November 24 • 10:00 AM

Why Are Patients Drawn to Certain Doctors?

We look for an emotional fit between our physicians and ourselves—and right now, that’s the best we can do.


November 24 • 8:00 AM

Why Do We Elect Corrupt Politicians?

Voters, it seems, are willing to forgive—over and over again—dishonest yet beloved politicians if they think the job is still getting done.



November 24 • 6:00 AM

They Steal Babies, Don’t They?

Ethiopia, the Hague, and the rise and fall of international adoption. An exclusive investigation of internal U.S. State Department documents describing how humanitarian adoptions metastasized into a mini-industry shot through with fraud, becoming a source of income for unscrupulous orphanages, government officials, and shady operators—and was then reined back in through diplomacy, regulation, and a brand-new federal law.


November 24 • 4:00 AM

Nudging Drivers, and Pedestrians, Into Better Behavior

Daniel Pink’s new series, Crowd Control, premieres tonight on the National Geographic Channel.


November 21 • 4:00 PM

Why Are America’s Poorest Toddlers Being Over-Prescribed ADHD Drugs?

Against all medical guidelines, children who are two and three years old are getting diagnosed with ADHD and treated with Adderall and other stimulants. It may be shocking, but it’s perfectly legal.



November 21 • 2:00 PM

The Best Moms Let Mess Happen

That’s the message of a Bounty commercial that reminds this sociologist of Sharon Hays’ work on “the ideology of intensive motherhood.”


November 21 • 12:00 PM

Eating Disorders Are Not Just for Women

Men, like women, are affected by our cultural preoccupation with thinness. And refusing to recognize that only makes things worse.


November 21 • 10:00 AM

Queens of the South

Inside Asheville, North Carolina’s 7th annual Miss Gay Latina pageant.


Follow us


Geography, Race, and LOLs

The online lexicon spreads through racial and ethnic groups as much as it does through geography and other traditional linguistic measures.

Feeling—Not Being—Wealthy Cuts Support for Economic Redistribution

A new study suggests it's relative wealth that leads people to oppose taxing the rich and giving to the poor.

Sufferers of Social Anxiety Disorder, Your Friends Like You

The first study of friends' perceptions suggest they know something's off with their pals but like them just the same.

Standing Up for My Group by Kicking Yours

Members of a minority ethnic group are less likely to express support for gay equality if they believe their own group suffers from discrimination.

How Old Brains Learn New Tricks

A new study shows that the neural plasticity needed for learning doesn't vanish as we age—it just moves.

The Big One

One in two United States senators and two in five House members who left office between 1998 and 2004 became lobbyists. November/December 2014

Copyright © 2014 by Pacific Standard and The Miller-McCune Center for Research, Media, and Public Policy. All Rights Reserved.