Why condensed matter physicists reject reductionism

Reduction is an approach that has been successful in science but is not itself synonymous with "science."

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  • Reductionism — the philosophical position that all phenomena can be explained by interactions between particles — is not inherently a part of the scientific method.
  • For example, most biological processes cannot be explained by appealing to quarks.
  • Those who study complex phenomena, such as condensed matter physicists, often reject reductionism and embrace its alternative, known as emergence.

Fundamentally, science is a path to understanding the world. It's a way to enter a dialogue with nature. Using the methods of science, certain kinds of questions — meaning questions that are posed in a particular kind of way — can get answered. Science is so successful at this question-answering task, however, that other ideas often get attached to it in a philosophical game of pin-the-tail-on-the-donkey. It's in this often unconscious association that ideas that are not fundamentally part of the method we call science get tagged as "what science says."

Reductionism vs. emergence

One of these ride-along ideas is reductionism. Reductionism is a philosophical stance that claims that any explanation about the universe must reduce to the fundamental entities of physics, things like quarks and electrons.

Not long ago, I wrote an article about why reductionism is not what science "says" about the world. I introduced reductionism's philosophical alternative, known as emergence, and I promised to write more and continue unpacking the tension between these views. Today, as promised, we will dig a bit deeper into this ancient and critical question.

My post sparked some lovely conversations. Some folks agreed with what I was saying; others most certainly did not. That was pretty awesome from my point of view because conversations among people who disagree are the only way each side can learn more about their own points of view (and maybe have their minds changed). Based on that discussion, astronomer Jason Wright penned a cogent post on his perspective on reductionism. Later, Wright's post led to a really lovely piece by philosophers Thomas Metcalf and Chelsea Harami that laid out the reductionism vs. emergence debate. Those articles are worth reading.

Here's a summary of the debate: Emergence argues that, sometimes, when the fundamental entities of physics combine, they create fundamentally new kinds of behaviors and structures. Emergence argues that nature invents new things at higher levels of structure (hence, my claim that you are more than your atoms).

Philosophers then go on to distinguish between weak and strong emergence. Weak emergence sees all causes still being tracked back to the atoms, while strong emergence wants to claim that something truly new emerges at the higher levels. Also, much of this debate happens within a philosophical framework called "physicalism," which claims that everything that exists is, well, physical.

Conscious experience, and to a lesser degree life, are often identified as Ur-examples of strong emergence. Conscious experience is so weird that you can see why it's easy to tag it as an emergent phenomenon. But what about emergence — either strong or weak — in plain old physics?

Emergence in condensed matter physics

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Perhaps unsurprisingly, some philosophers argue "yes," and others argue "no." For those with a physics background, I highly recommend the book Why More Is Different: Philosophical Issues in Condensed Matter Physics and Complex Systems for some good articles on the subject.

One of the most interesting things about the emergence-vs-reductionism debate is who takes which side. It is most definitely worth noting that some of the most emphatic voices arguing for stronger versions of emergence come from condensed matter physicists. This is the field that studies solid matter (and liquids too). In fact, the whole debate got started in 1972 with a paper by Noble Prize-winning physicist Philip Anderson called "More is Different," in which he wrote:

"The reductionist hypothesis does not by any means imply a 'constructionist' one: The ability to reduce everything to simple fundamental laws does not imply the possibility to start from those laws and reconstruct the universe. (...) At each level of complexity entirely new properties appear, and the understanding of the new behaviors requires research which I think is as fundamental in its nature as any other."

Later Robert Laughlin, also a condensed matter physicist, wrote a book called A Different Universe, in which he argued that attempts to apply the fundamental equations of quantum mechanics to any system with more than 100 particles leaves you with something that can only be solved with God's computer (i.e., it can't really be solved). Based on this, he argued that you really can't derive the higher levels of structure from the lower levels and that there do exist higher order, emergent principles that are required to understand the world.

Another Nobel Prize winning condensed matter physicist Anthony Leggett has also weighed in on this question, writing:

"No significant advance in the theory of matter in bulk has ever come about through derivation from microscopic principles. (...) I would confidently argue further that it is in principle and forever impossible to carry out such a derivation. (...) The so-called derivations of the results of solid-state physics from microscopic principles alone are almost all bogus, if 'derivation' is meant to have anything like its usual sense."

Leggett goes farther:

"I claim then that the important advances in macroscopic physics come essentially in the construction of models at an intermediate or macroscopic level, and that these are logically (and psychologically) independent of microscopic physics."

Reductionism doesn't work

What is interesting to me is that it's the people who actually do the work in studying the higher levels of structure that are often the ones most convinced that reductionism doesn't really work. Now physicists are not philosophers, which means that they are not trained to see the ontological and epistemological meaning of the theories they create. But I do think it's telling that those closest to complexity have the deepest intuitions of and commitments to emergence.

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COVID and "gain of function" research: should we create monsters to prevent them?

Gain-of-function mutation research may help predict the next pandemic — or, critics argue, cause one.

Credit: Guillermo Legaria via Getty Images

This article was originally published on our sister site, Freethink.

"I was intrigued," says Ron Fouchier, in his rich, Dutch-accented English, "in how little things could kill large animals and humans."

It's late evening in Rotterdam as darkness slowly drapes our Skype conversation.

This fascination led the silver-haired virologist to venture into controversial gain-of-function mutation research — work by scientists that adds abilities to pathogens, including experiments that focus on SARS and MERS, the coronavirus cousins of the COVID-19 agent.

If we are to avoid another influenza pandemic, we will need to understand the kinds of flu viruses that could cause it. Gain-of-function mutation research can help us with that, says Fouchier, by telling us what kind of mutations might allow a virus to jump across species or evolve into more virulent strains. It could help us prepare and, in doing so, save lives.

Many of his scientific peers, however, disagree; they say his experiments are not worth the risks they pose to society.

A virus and a firestorm

The Dutch virologist, based at Erasmus Medical Center in Rotterdam, caused a firestorm of controversy about a decade ago, when he and Yoshihiro Kawaoka at the University of Wisconsin-Madison announced that they had successfully mutated H5N1, a strain of bird flu, to pass through the air between ferrets, in two separate experiments. Ferrets are considered the best flu models because their respiratory systems react to the flu much like humans.

The mutations that gave the virus its ability to be airborne transmissible are gain-of-function (GOF) mutations. GOF research is when scientists purposefully cause mutations that give viruses new abilities in an attempt to better understand the pathogen. In Fouchier's experiments, they wanted to see if it could be made airborne transmissible so that they could catch potentially dangerous strains early and develop new treatments and vaccines ahead of time.

The problem is: their mutated H5N1 could also cause a pandemic if it ever left the lab. In Science magazine, Fouchier himself called it "probably one of the most dangerous viruses you can make."

Just three special traits

Recreated 1918 influenza virionsCredit: Cynthia Goldsmith / CDC / Dr. Terrence Tumpey / Public domain via Wikipedia

For H5N1, Fouchier identified five mutations that could cause three special traits needed to trigger an avian flu to become airborne in mammals. Those traits are (1) the ability to attach to cells of the throat and nose, (2) the ability to survive the colder temperatures found in those places, and (3) the ability to survive in adverse environments.

A minimum of three mutations may be all that's needed for a virus in the wild to make the leap through the air in mammals. If it does, it could spread. Fast.

Fouchier calculates the odds of this happening to be fairly low, for any given virus. Each mutation has the potential to cripple the virus on its own. They need to be perfectly aligned for the flu to jump. But these mutations can — and do — happen.

"In 2013, a new virus popped up in China," says Fouchier. "H7N9."

H7N9 is another kind of avian flu, like H5N1. The CDC considers it the most likely flu strain to cause a pandemic. In the human outbreaks that occurred between 2013 and 2015, it killed a staggering 39% of known cases; if H7N9 were to have all five of the gain-of-function mutations Fouchier had identified in his work with H5N1, it could make COVID-19 look like a kitten in comparison.

H7N9 had three of those mutations in 2013.

Gain-of-function mutation: creating our fears to (possibly) prevent them

Flu viruses are basically eight pieces of RNA wrapped up in a ball. To create the gain-of-function mutations, the research used a DNA template for each piece, called a plasmid. Making a single mutation in the plasmid is easy, Fouchier says, and it's commonly done in genetics labs.

If you insert all eight plasmids into a mammalian cell, they hijack the cell's machinery to create flu virus RNA.

"Now you can start to assemble a new virus particle in that cell," Fouchier says.

One infected cell is enough to grow many new virus particles — from one to a thousand to a million; viruses are replication machines. And because they mutate so readily during their replication, the new viruses have to be checked to make sure it only has the mutations the lab caused.

The virus then goes into the ferrets, passing through them to generate new viruses until, on the 10th generation, it infected ferrets through the air. By analyzing the virus's genes in each generation, they can figure out what exact five mutations lead to H5N1 bird flu being airborne between ferrets.

And, potentially, people.

"This work should never have been done"

The potential for the modified H5N1 strain to cause a human pandemic if it ever slipped out of containment has sparked sharp criticism and no shortage of controversy. Rutgers molecular biologist Richard Ebright summed up the far end of the opposition when he told Science that the research "should never have been done."

"When I first heard about the experiments that make highly pathogenic avian influenza transmissible," says Philip Dormitzer, vice president and chief scientific officer of viral vaccines at Pfizer, "I was interested in the science but concerned about the risks of both the viruses themselves and of the consequences of the reaction to the experiments."

In 2014, in response to researchers' fears and some lab incidents, the federal government imposed a moratorium on all GOF research, freezing the work.

Some scientists believe gain-of-function mutation experiments could be extremely valuable in understanding the potential risks we face from wild influenza strains, but only if they are done right. Dormitzer says that a careful and thoughtful examination of the issue could lead to processes that make gain-of-function mutation research with viruses safer.

But in the meantime, the moratorium stifled some research into influenzas — and coronaviruses.

The National Academy of Science whipped up some new guidelines, and in December of 2017, the call went out: GOF studies could apply to be funded again. A panel formed by Health and Human Services (HHS) would review applications and make the decision of which studies to fund.

As of right now, only Kawaoka and Fouchier's studies have been approved, getting the green light last winter. They are resuming where they left off.

Pandora's locks: how to contain gain-of-function flu

Here's the thing: the work is indeed potentially dangerous. But there are layers upon layers of safety measures at both Fouchier's and Kawaoka's labs.

"You really need to think about it like an onion," says Rebecca Moritz of the University of Wisconsin-Madison. Moritz is the select agent responsible for Kawaoka's lab. Her job is to ensure that all safety standards are met and that protocols are created and drilled; basically, she's there to prevent viruses from escaping. And this virus has some extra-special considerations.

The specific H5N1 strain Kawaoka's lab uses is on a list called the Federal Select Agent Program. Pathogens on this list need to meet special safety considerations. The GOF experiments have even more stringent guidelines because the research is deemed "dual-use research of concern."

There was debate over whether Fouchier and Kawaoka's work should even be published.

"Dual-use research of concern is legitimate research that could potentially be used for nefarious purposes," Moritz says. At one time, there was debate over whether Fouchier and Kawaoka's work should even be published.

While the insights they found would help scientists, they could also be used to create bioweapons. The papers had to pass through a review by the U.S. National Science Board for Biosecurity, but they were eventually published.

Intentional biowarfare and terrorism aside, the gain-of-function mutation flu must be contained even from accidents. At Wisconsin, that begins with the building itself. The labs are specially designed to be able to contain pathogens (BSL-3 agricultural, for you Inside Baseball types).

They are essentially an airtight cement bunker, negatively pressurized so that air will only flow into the lab in case of any breach — keeping the viruses pushed in. And all air in and out of the lap passes through multiple HEPA filters.

Inside the lab, researchers wear special protective equipment, including respirators. Anyone coming or going into the lab must go through an intricate dance involving stripping and putting on various articles of clothing and passing through showers and decontamination.

And the most dangerous parts of the experiment are performed inside primary containment. For example, a biocontainment cabinet, which acts like an extra high-security box, inside the already highly-secure lab (kind of like the radiation glove box Homer Simpson is working in during the opening credits).

"Many people behind the institution are working to make sure this research can be done safely and securely." — REBECCA MORITZ

The Federal Select Agent program can come and inspect you at any time with no warning, Moritz says. At the bare minimum, the whole thing gets shaken down every three years.

There are numerous potential dangers — a vial of virus gets dropped; a needle prick; a ferret bite — but Moritz is confident that the safety measures and guidelines will prevent any catastrophe.

"The institution and many people behind the institution are working to make sure this research can be done safely and securely," Moritz says.

No human harm has come of the work yet, but the potential for it is real.

"Nature will continue to do this"

They were dead on the beaches.

In the spring of 2014, another type of bird flu, H10N7, swept through the harbor seal population of northern Europe. Starting in Sweden, the virus moved south and west, across Denmark, Germany, and the Netherlands. It is estimated that 10% of the entire seal population was killed.

The virus's evolution could be tracked through time and space, Fouchier says, as it progressed down the coast. Natural selection pushed through gain-of-function mutations in the seals, similarly to how H5N1 evolved to better jump between ferrets in his lab — his lab which, at the time, was shuttered.

"We did our work in the lab," Fouchier says, with a high level of safety and security. "But the same thing was happening on the beach here in the Netherlands. And so you can tell me to stop doing this research, but nature will continue to do this day in, day out."

Critics argue that the knowledge gained from the experiments is either non-existent or not worth the risk; Fouchier argues that GOF experiments are the only way to learn crucial information on what makes a flu virus a pandemic candidate.

"If these three traits could be caused by hundreds of combinations of five mutations, then that increases the risk of these things happening in nature immensely," Fouchier says.

"With something as crucial as flu, we need to investigate everything that we can," Fouchier says, hoping to find "a new Achilles' heel of the flu that we can use to stop the impact of it."

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