There’s Something Called “Quantum Biology”

Occasionally you hear some news and wonder “Why didn’t I ever hear about this before?” That was my reaction to the news that scientists have been investigating something called “quantum biology” for the past 20 years or so.

Last week, there was a link on the always interesting Self Aware Patterns blog to a Guardian article called “You’re Powered by Quantum Mechanics. No, Really…”. The article was written by two scientists, the physicist Jim Al-Khalili and the geneticist Johnjoe McFadden. Here’s the news I found extremely surprising:

As 21st-century biology probes the dynamics of ever-smaller systems – even individual atoms and molecules inside living cells – the signs of quantum mechanical behaviour in the building blocks of life are becoming increasingly apparent. Recent research indicates that some of life’s most fundamental processes do indeed depend on weirdness welling up from the quantum undercurrent of reality.

Really? People with various qualifications have speculated for years about quantum mechanical phenomena occurring in the human brain, usually in an attempt to justify belief in free will. But this is real science based on experimental results (albeit with a dose of speculation too).

The McFadden/Al-Khalili article cites three examples in which quantum phenomena appear to play a crucial role in biology. First, enzymes appear to work via quantum tunneling:

Enzymes … speed up chemical reactions so that processes that would otherwise take thousands of years proceed in seconds inside living cells. Life would be impossible without them. But how they accelerate chemical reactions by such enormous factors, often more than a trillion-fold, has been an enigma. Experiments over the past few decades, however, have shown that enzymes make use of a remarkable trick called quantum tunnelling to accelerate biochemical reactions. Essentially, the enzyme encourages electrons and protons to vanish from one position in a biomolecule and instantly rematerialise in another, without passing through the gap in between – a kind of quantum teleportation. 

Second, photosynthesis seems to involve wave/particle duality:

The first step in photosynthesis is the capture of a tiny packet of energy from sunlight that then has to hop through a forest of chlorophyll molecules …. The problem is understanding how the packet of energy appears to so unerringly find the quickest route through the forest. An ingenious experiment … revealed that the energy packet was not hopping haphazardly about, but performing a neat quantum trick. Instead of behaving like a localised particle travelling along a single route, it behaves quantum mechanically, like a spread-out wave, and samples all possible routes at once to find the quickest way.

Third, there are animals who appear to rely on quantum entanglement:

A third example of quantum trickery in biology … is the mechanism by which birds and other animals make use of the Earth’s magnetic field for navigation. Studies of the European robin suggest that it has an internal chemical compass that utilises an astonishing quantum concept called entanglement, which Einstein dismissed as “spooky action at a distance”. This phenomenon describes how two separated particles can remain instantaneously connected via a weird quantum link. The current best guess is that this takes place inside a protein in the bird’s eye, where quantum entanglement makes a pair of electrons highly sensitive to the angle of orientation of the Earth’s magnetic field, allowing the bird to “see” which way it needs to fly.

McFadden has published another article at Aeon in which he further discusses the examples above and throws in a possible relationship between quantum mechanics and the sense of smell. In addition, a quick search online turned up an article from the MIT Technology Review explaining how quantum entanglement may stop large DNA molecules from falling apart and an overview of developments in quantum biology from the BBC.

Not everyone is convinced of the quantum nature of these phenomena, of course, and research continues. Still, I think this is all extremely interesting. In one sense, it’s surprising that living things could employ phenomena like entanglement and quantum tunneling that seem so bizarre and so removed from ordinary life. But in another sense, it shouldn’t be a surprise if millions of years of evolution have allowed both plants and animals to take advantage of such powerful and fundamental natural phenomena.

A Guide to Reality, Part 8

Chapter 3 of Alex Rosenberg’s The Atheist’s Guide to Reality is called “How Physics Fakes Design”, although Professor Rosenberg would be the first to object that physics isn’t the kind of thing that can fake anything. His point, of course, is that everything that looks like it’s been designed in the natural world (the human eye, for example) is merely the result of activity at the atomic and molecular level, which itself results from subatomic particles doing what they normally do.

In fact, Professor Rosenberg holds that things that really were designed (like your computer) are the result of the very same natural laws. Design, wherever it appears to occur, whether the result of evolution or conscious effort, is just another illusion. 

In this chapter, however, Rosenberg is focused on evolutionary adaptation:

If the physical facts fix all the facts, then the emergence and persistence of adaptations had better result from the laws of physics alone. In fact, they had better be the result of the operation of thermodynamics. Otherwise we will have to admit that there is more going on in the universe than physics tells us there is. Some physicists may be okay with this, but scientism has to reject it. We need to show that the process Darwin discovered starts with zero adaptations and builds them all as the result of the laws of physics alone. (51-52).

Rosenberg begins by offering a statement of the three essential features of the theory of natural selection, as stated by the biologist Richard Lewontin:

  1. There is always variation in the traits of organisms, genes, hives, groups or whatever it is that replicates or reproduces;
  2. The variant traits differ in fitness;
  3. The fitness differences among some of the traits are inherited.

As Rosenberg explains, the replication or reproduction that occurs in nature doesn’t always result in an exact copy being made (mutations occur, for example). He prefers calling this “blind variation” instead of “random variation” to emphasize the point that nature doesn’t cause these variations on purpose. Most such variations yield no benefit. Occasionally, one does. A “beneficial” variation is one that tends to be passed on to the next generation. Given enough time, such variations can result in complex structures like the eye. Evolution occurs.  

Getting back to physics, Rosenberg argues that the second law of thermodynamics (closed systems tend toward disorder) makes natural selection “inevitable” (although at the end of the chapter he says that the second law only makes it “possible”). He admits that the relationship between the second law and natural selection is puzzling, since natural selection seems to increase the amount of order or organization in the world. But he quickly disposes of this objection by pointing out that the second law only requires a “net increase” in disorder over time. Organization will occasionally increase, but almost always at the cost of more disorganization elsewhere (as when organisms grow by digesting food).

Next, in the space of 11 interesting pages, Rosenberg shows how molecular activity, all subject to the second law, results in what he calls “molecular evolution” (69). As he explains it, there is a lot of “thermodynamic noise” in the universe. Molecules are constantly copying themselves, sometimes imperfectly, and forming bonds with each other. These processes result in new molecular forms. Some molecules are more stable than others, meaning that they will tend to last longer in particular chemical environments. As environments change, however, certain molecules become less stable and break apart, while others come together, just as organisms adapt or fail to adapt to changes in their environments. These various processes satisfy the criteria for evolution described above:

Natural selection requires … reproduction, variation and inheritance. It doesn’t really care how any of these three things get done, just so long as each one goes on long enough to get some adaptations. Reproduction doesn’t have to be sexual or asexual or even easily recognized by us to be reproduction. Any kind of replication is enough (59).

The same goes for variation and inheritance. I would add that these processes must occur in an environment filled with enough matter and energy to keep things moving along. Then, through the course of countless such chemical interactions over immense periods of time, complex organic molecules can develop:

Thermodynamic noise constantly makes more and more different environments – different temperatures, different pH, different concentrations of chemicals, different amounts of water or oxygen or nitrogen, or more complicated acids and bases, magnetic fields and radiation. As a result, there will be a corresponding selection for more and more different molecules (69).

And here we are today, each of us a collection of atoms and molecules, each doing its individual thing:

And so on up the ladder of complexity and diversity that produces assemblies of molecules so big they become recognizable as genes, viruses, organelles, cells, tissues, organs, organisms … and us (69).

Not being a scientist myself, I can’t vouch for Rosenberg’s account of how all this works. However, it all sounds plausible to me. If you read the chapter, you will probably feel the same way.

One closing comment: people who don’t accept the fact that natural selection could eventually lead to a particular complex entity usually argue that such a thing couldn’t possibly happen. It’s inconceivable, they might say, that the human eye, which needs a bunch of parts that work together in order to work at all, could have resulted from a long series of evolutionary steps. It was Charles Darwin himself who offered the human eye as the biggest challenge to his theory. Rosenberg mentions this issue near the beginning of this chapter but doesn’t return to it. His goal in chapter 3 is to show how adaptation gets started, not how far it can go. I think, however, that it’s unwise to bet against science in its pursuit of explanations for mysterious things like the human eye or consciousness. Too many phenomena that used to be mysterious have already been explained.

In our next installment (assuming I stay sufficiently motivated): Good design isn’t just an illusion, it’s also rare, expensive and accidental.

A Guide to Reality, Part 5

Alex Rosenberg, the author of The Atheist’s Guide to Reality, argues that “we should embrace physics as the whole truth about reality”. On the face of it, that’s a remarkable statement open to obvious challenges. 

Rosenberg, however, acknowledges that parts of physics are relatively speculative, unsettled or even inconsistent. It’s the solidly-confirmed part of physics that he’s talking about, the part of physics that is “finished” and “explains almost everything in the universe – including us”. What he’s really claiming, therefore, is that settled physics is the whole truth about reality. 

But is settled physics actually true? Philosophers disagree about what science is, what truth is and, not surprisingly, how close science gets to the truth, but I agree with Rosenberg that settled physics seems to be true. The predictions of special relativity, for example, appear to be 100% correct. (This isn’t to deny that some settled physics might become unsettled one day.) As evidence of the reliability of physics, Rosenberg points out how precise some predictions are: “quantum electrodynamics predicts the mass and charge of subatomic particles to 12 decimal places”. Those predictions are “true” in any reasonable sense of the word, even if physicists eventually refine their predictions to even more decimal places.

Some philosophers and scientists don’t accept Rosenberg’s “scientific realist” view, however. They think science is merely a tool that allows us to get things done. Questions like whether electrons or other theoretical entities really exist as physics describes them are put aside, since they’re viewed as unanswerable and irrelevant. Personally, I think physics allows us to get things done because it’s true, and furthermore it’s true in the sense that the objects and events physics describes are real, whether they’re observable or not. I believe that’s Rosenberg’s opinion too.

The second, more interesting challenge to Rosenberg’s view of physics concerns his claim that settled physics is the “whole” truth about reality. Clearly, there are mathematical and logical truths, which aren’t part of physics, but I take Rosenberg to be referring to truths about the universe and its contents, i.e. “real” stuff.

Nevertheless, if physics isn’t finished, it can’t be the “whole” truth. There must be some physical truths yet to be discovered (for example, what’s the story on dark matter and dark energy, two big things we know little about?). So Rosenberg’s claim that we should embrace settled physics as the whole truth about reality should really be understood as “settled physics is the only truth about reality we currently have”.  

Two obvious questions remain, however. Do we discover the truth from sciences other than physics? And do we learn anything true about the world even when we aren’t doing science?

Well, most people would agree that chemistry, for example, is a science that gets at the truth if any science does. Rosenberg clearly knows about chemistry, so why would he deny that chemistry is as valid as physics? The answer is that he thinks physics has shown there is nothing in the universe except fermions (e.g. quarks) and bosons (e.g. photons). From the idea that fermions and bosons are the only things that really exist, he concludes that all of reality can be explained in terms of those sub-atomic particles. After all, everything in the universe involves elementary particles being somewhere or doing something. Since physics is the science that tells us all about elementary particles and what they do, it’s the fundamental science. Using physics, therefore, we can explain chemistry, which we can then use to explain biology. Another way of saying this is that biology is reducible to chemistry and chemistry is reducible to physics. Knowledge of physics is the only knowledge that counts, because “the physical facts fix all the facts”, including chemical and biological facts.

The big problem with this point of view, aside from the difficulty in actually carrying out such reductions (replacing chemistry with physics, for example) is that fermions and bosons do such interesting things when they interact or are arranged in certain ways. Put some together and you have atoms; put some atoms together and you have molecules; put some of them together and you have cells. Once low-level particles are arranged as, for example, clouds or baseballs or trees, patterns or regularities in the behavior of these higher-level entities emerge. There are new facts to be learned.

If the universe were merely a collection of sub-atomic particles randomly scattered about, there wouldn’t be any chemical or biological facts for chemists and biologists to discover. But the particles in our universe aren’t randomly scattered. They’ve clumped together in various ways. Acquiring knowledge about these clumps (of which you and I are examples) is what chemists, biologists and other scientists (geologists, astronomers, psychologists, etc.) do. Rosenberg knows this, of course, but for some reason downplays it, choosing to focus on physics as the sine qua non of science. In virtue of its power and generality, physics should be embraced as the most fundamental science, but it clearly isn’t the only science worth embracing. 

The other question raised by Rosenberg’s scientism (or physics-ism) is whether we can add to our knowledge when we aren’t doing science at all. Rosenberg doesn’t seem to think so. Although science is built on observation, he is extremely skeptical about what can be learned by simply looking and listening. He also seriously mistrusts introspection. More on this later. 

Next: The 2nd Law of Thermodynamics and us.

A Guide to Reality, Part 4

Chapter 2 of The Atheist’s Guide to Reality is probably the key chapter in the book. That’s where Professor Rosenberg lays out his view of physics and the nature of reality. He doesn’t mince words:

Everything in the universe is made up of the stuff that physics tells us fills up space, including the spaces that we fill up. And physics can tell us how everything in the universe works, in principle and in practice, better than anything else. Physics catalogs all the basic kinds of things that there are and all the things that can happen to them (21).

According to Rosenberg, “we should embrace physics as the whole truth about reality”. Why? Because science is a cumulative process, in which findings are confirmed, corrected or refuted, resulting in a solid foundation. Physicists are still learning things, but the “part of [physics] that explains almost everything in the universe – including us – is finished, and much of it has been finished for a century or more” (21).

Physicists, in particular, have discovered that everything in the universe is composed of either fermions (such as quarks, electrons and neutrinos) and bosons (like photons and gluons), and combinations thereof (like protons and molecules). Fermions are usually associated with matter, while bosons are usually associated with fields and forces. Rosenberg says that’s all there is:

All the processes in the universe, from atomic to bodily to mental, are purely physical processes involving fermions and bosons interacting with one another…Physical theory explains and predicts almost everything to inconceivably precise values over the entire body of data available…From a small number of laws, physics can neatly explain the whole trajectory of the universe and everything in it…The phenomenal accuracy of its prediction, the unimaginable power of its technological application, and the breathtaking extent and detail of its explanations are powerful reasons to believe that physics is the whole truth about reality (21-25).

But what about the other sciences? Surely, chemistry and biology, for example, say something true about reality. Rosenberg, however, argues that physics explains chemistry and chemistry explains biology. Everything that happens in your body is a chemical process, and every chemical process is a physical process:

The only causes in the universe are physical, and everything in the universe that has a cause has a physical cause. In fact, we can go further and confidently assert that the physical facts fix all the facts … including the chemical, biological, psychological, social, economic, political and other human facts (25-26).

He left out the geological and cosmological, but you get the idea. Higher-level sciences are in principle reducible to lower-level sciences. Philosophers call this view “reductionism”. Rosenberg is clearly a “reductionist” of some sort. A similar claim is that all higher-level facts depend or “supervene” on lower-level facts (this principle is called “supervenience”). Rosenberg asks us to imagine two regions of space-time, our own plus another millions of light-years away, in which every fermion and boson is arranged exactly the same way. In such a case, everything else in the two regions would be the same too. Regardless of the regions’ respective histories, if all the sub-atomic particles are arranged the same way, the two regions will contain the same rocks, the same birds and bees, the same political institutions, the same music, the same people with the same memories and thoughts. Physics fixes all the facts.

Next time, before continuing with chapter 2, we’ll consider whether it’s reasonable to “embrace physics as the whole truth about reality”.