There’s Something Called “Quantum Biology”

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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.

To Vote Or Not To Vote – An Easy Question

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I always vote and plan to keep voting until the Republicans find a way to stop me. It’s not that I think my single vote will make a difference. It’s almost guaranteed not to. But voting is a ritual of democracy – something we do to participate in and demonstrate our support for our (ailing) system of government. Even though it’s very likely a waste of time.

From Wikipedia:

A ritual “is a sequence of activities involving gestures, words, and objects, performed in a sequestered place, and performed according to set sequence”. Rituals may be prescribed by the traditions of a community, including a religious community. Rituals are characterized by formalism, traditionalism, invariance, rule-governance, sacral symbolism and performance….

The field of ritual studies has seen a number of conflicting definitions of the term. One given by Kyriakidis is that a ritual is an outsider’s … category for a set activity (or set of actions) that, to the outsider, seems irrational, non-contiguous, or illogical.

Nevertheless, it would be nice if we practiced more majority rule in this country. Here Ezra Klein answers the question: “How can Republicans be less popular than Democrats yet headed for a landslide?”.

A reasonable person might stay home after reading that, but Mr. Klein believes “There are 9 damn good reasons to go vote today”.

Plus there’s that other important reason he doesn’t mention: It’s a ritual of democracy!

The Extremely Special Third Realm

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The German mathematician, logician and part-time philosopher Gottlob Frege (1848-1925) wasn’t well-known during his lifetime, but he’s now considered the father of analytic philosophy, the type of philosophy most professors in English-speaking countries and Scandinavia do. (Being the father of analytic philosophy makes you very well-known in certain circles.)

In 1918, Frege published an article called “The Thought” (Der Gedanke), in which he drew an interesting distinction. In addition to the standard categories of the mental and the physical, Frege said that “a third realm must be recognized”. This is the realm of meaning or sense that’s independent of anyone’s particular ideas.

First, therefore, is the realm of spatiotemporal things (“such as trees, stones and houses”). Then there is the realm of particular ideas in specific people’s minds (“an inner world distinct from the outer world, a world of sense impressions, of creations of [the] imagination, of sensations, of feelings and moods”). Lastly, there is the realm of what Frege called “thought”. The occupants of this third realm are similar to ideas, in that they “cannot be perceived by the senses”, but they are also similar to things, in that they “need no bearer”, i.e. they need not exist in anyone’s mind. 

Thus, the thought [expressed by the Pythagorean theorem, for example] is timelessly true, true independently of whether anyone takes it to be true. It needs no bearer. It is not true for the first time when it is discovered….

It’s only because there is a single, commonly accessible thought that expresses the Pythagorean theorem that each of us can refer to it (the identical theorem) and agree or disagree about its truth value. Otherwise, my Pythagorean theorem would differ from yours, since the particular ideas in my mind are always and necessarily my ideas and never yours (and vice versa). 

Indeed, the fact that we are able to use language to agree or disagree about particular propositions is evidence that this third realm exists:

If it is not the same thought … which is taken to be the content of the Pythagorean theorem by me and by another person, one should not really say “the Pythagorean theorem” but “my Pythagorean theorem, “his Pythagorean theorem”, and these would be different.

According to Frege, the thoughts that inhabit this third realm aren’t all propositions of mathematics or logic. He asks us to consider a statement like “This tree had green leaves”. Once we specify a time — “This tree had green leaves on July 1, 2004” — we have a statement that expresses a thought, which “if it is true, is true not only today or tomorrow but timelessly”.

Personally, I don’t find Frege’s notion of a third realm terribly convincing. I think there’s only one realm that has anything in it. But, as a metaphor, the “third realm” captures something extremely important. Along the same lines, the philosopher Charlie Huenemann recently began a post called “Reality Is Down the Hall” by quoting Schopenhauer:

“It is therefore worth noting and indeed wonderful to see, how man, besides his life in the concrete, always lives a second life in the abstract.”

Schopenhauer’s “second life” has this in common with Frege’s “third realm”: they both evoke what philosophers now call “abstract entities” or “abstract objects”:

Thus it is universally acknowledged that numbers and the other objects of pure mathematics are abstract (if they exist), whereas rocks and trees and human beings are concrete. Some clear cases of abstracta are classes, propositions, concepts, the letter ‘A’, and Dante’s Inferno. Some clear cases of concreta are stars, protons, electromagnetic fields, the chalk tokens of the letter ‘A’ written on a certain blackboard, and James Joyce’s copy of Dante’s Inferno. [Stanford Encyclopedia of Philosophy]

Instead of “realms” or “lives”, however, Huenemann refers to the concrete and abstract “worlds” in which we live:

One world is at our fingertips, at the tips of our tongues, and folded into our fields of vision. The concrete world is just the world; and the more we try to describe it, the more we fail, as the here and now is immeasurably more vivid than the words “here” and “now” could ever suggest…. 

The second world is the one we encounter just as soon as we begin thinking and talking about the here and now. It is such stuff as dreams are made on; its substance is concept, theory, relation.

He then describes how we construct models of the concrete world, in particular, how scientists construct models that are increasingly intricate. He quotes Sir Arthur Eddington’s famous description of two tables:

[One table] has extension; it is comparatively permanent; it is coloured; above all it is substantial. By substantial I do not merely mean that it does not collapse when I lean upon it; I mean that it is constituted of “substance” and by that word I am trying to convey to you some conception of its intrinsic nature. It is a thing; not like space, which is a mere negation; nor like time, which is – Heaven knows what! … I do not think substantiality can be described better than by saying that it is the kind of nature exemplified by an ordinary table…. 

My scientific table is mostly emptiness. Sparsely scattered in that emptiness are numerous electric charges rushing about with great speed; but their combined bulk amounts to less than a billionth of the bulk of the table itself. Notwithstanding its strange construction it turns out to be an entirely efficient table. It supports my writing paper as satisfactorily as table No. 1; for when I lay the paper on it the little electric particles with their headlong speed keep on hitting the underside, so that the paper is maintained in shuttlecock fashion at a nearly steady level. If I lean upon this table I shall not go through; or, to be strictly accurate, the chance of my scientific elbow going through my scientific table is so excessively small that it can be neglected in practical life.

Huenemann points out that, “as educated beings”, we accept that the table described by science is “ultimately the real one”. He writes that the “second table somehow gives rise to the first table”, the one that seems perfectly solid from our human perspective. (At least, those of us who are “scientific realists” accept the ultimate reality of the second table, unlike those sometimes called “instrumentalists” who think the theoretical entities of science are merely useful devices for coping with the world.)

But then Hueneman seems to question our belief in the reality of the second, scientific table: 

…here is an odd inversion – the first table, the one in the concrete world, is not quite as fully real as the abstract and dreamy second table, the one we never actually see, the one that is supposed to be a swarm of charged gnats, or packets of probabilities. The concrete table turns out to be an illusion. It arises somehow from the abstract world as does a mirage from heat and the bending of light. Isn’t that remarkable? Our official policy is to take the abstract to be more real than the concrete.

But, of course, the second, scientific table isn’t abstract or dreamy at all. It’s true that we can’t perceive it, but if the physicists are correct, it’s completely concrete. Instead, it’s the physicists’ description of the table, the theory of atoms and electrons, that’s abstract. Using Frege’s terminology, the meaningful propositions that scientifically describe the table belong to the third realm; the subatomic particles in the table, the marks in physics textbooks and the table in your dining room are concrete and belong to the first realm; and the particular ideas you and I have in our minds about such things belong to the second realm. It’s only the third realm of meaning or sense that is abstract. It’s abstract but, according to Frege, very real, even though its reality “is of quite a different kind than that of things”.

In practical terms, of course, it makes little difference whether we say abstract objects like numbers and propositions exist or not. Nobody thinks they float around in some ethereal, non-spatiotemporal realm (it would be quite impressive if they did). However, the fact that we can think about such things, real or not, is obviously one of the characteristics that makes humanity special, maybe the only thing that makes us special.

Furthermore, we act as if abstract objects were real, treating them with the utmost respect. Where would we be without the number 7, for example? Or 3 or 19, for that matter? Where would you be without the abstract object that is your name? And how about the Golden Rule? Or the concepts of truth or justice? As Schopenhauer said, it’s remarkably wonderful that we live with such things.

An Israeli on Failure in Gaza and the Way Out

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Assaf Sharon, a philosophy professor at Tel Aviv University, has an article in the New York Review of Books concerning the recent violence in the Gaza Strip and the only realistic way to resolve the Israeli/Palestinian conflict. Below are extended selections from “Failure in Gaza”, which is available in full here:

“In Israel, endless controversy over Gaza has overlooked one question: How did we get here in the first place? Why, after a considerable period of relative calm, did Hamas resume rocket fire into Israel?”

“Before the current operation began, Hamas was at one of the lowest points in its history….In these circumstances, Hamas agreed last April to reconciliation with its political rival Fatah, based on Fatah’s terms. For example, the agreement called for a government of technocrats largely under the control of the Palestinian Authority led by Mahmoud Abbas.”

“But Benjamin Netanyahu viewed the reconciliation as a threat rather than an opportunity….He saw the reconciliation with Hamas as an opportunity to criticize the Palestinian president…. As soon as the reconciliation was announced, Netanyahu launched a public offensive against Palestinian unity and demanded that the international community oppose it….”

“Netanyahu could have chosen a different path. He could have used the reconciliation to reinforce Abbas’s position and further destabilize Hamas. He could, in recognition of the agreement, have encouraged Egypt to open its border with Gaza in order to demonstrate to Gazans that the Palestinian Authority offered a better life than Hamas. Instead, Israel prevented the transfer of salaries to 43,000 Hamas officials in Gaza, sending a clear message that Israel would not treat Gaza any differently under the rule of moderate technocrats from the Palestinian Authority.”

“The abduction of three Israeli youths in the West Bank on June 12 gave Netanyahu another opportunity to undermine the reconciliation…. Despite the statement by … the Hamas political bureau chief, that the Hamas political leadership did not know of the plans to carry out the abduction, Netanyahu was quick to lay the blame on Hamas, declaring that Israel had ‘unequivocal proof’ that the organization was involved in the abduction.”

“As yet, Israeli authorities have produced no such proof and the involvement of the Hamas leadership in the kidnapping remains unclear. While the individuals suspected of having carried out the kidnapping are associated with Hamas, some of the evidence suggests that they may have been acting on their own initiative and not under the direction of Hamas’s central leadership. Regardless of this, Netanyahu’s response, apparently driven by the ill-advised aim of undermining Palestinian reconciliation, was reckless.”

“Determined to achieve by force what he failed to accomplish through diplomacy, Netanyahu not only blamed Hamas, but linked the abduction to Palestinian reconciliation, as if the two events were somehow causally related. ‘Sadly, this incident illustrates what we have been saying for months,’ he stated, ‘that the alliance with Hamas has extremely grave consequences’. Israeli security forces were in possession of evidence strongly indicating the teens were dead, but withheld this information from the public until July 1….”

“On the prime minister’s orders, IDF forces raided Hamas’s civil and welfare offices throughout the West Bank and arrested hundreds of Hamas leaders and operatives. These arrests did not help to locate the abductors or their captives. Among the arrested were fifty-eight Palestinians previously released as part of the deal to return the Israeli soldier Gilad Shalit, who had been a captive of Hamas since 2006.”

“As part of this ill-conceived operation against Hamas, Israel also mounted air strikes on Hamas facilities in Gaza. Apparently, Hamas did not take an active part in firing rockets for more than two weeks, although it did not prevent other factions in Gaza from firing. Only on June 29 or 30 did Hamas restart the rocket bombardment of Israeli territory, which it had not engaged in since November 2012. Israel retaliated against Hamas in Gaza and a vicious cycle began. Netanyahu lost control over an escalation he had instigated. In his badly misjudged eagerness to blame Abbas and punish him for reconciling with Hamas, Netanyahu turned a vicious but local terrorist attack into a runaway crisis….”

….

“Israel’s conduct throughout the crisis has been based directly on Netanyahu’s philosophy of ‘conflict management’, whose underlying premise is that the conflict between Israelis and Palestinians cannot be solved, but can be effectively ‘managed’ for a very long period of time. This feeble, not to mention defeatist, assumption is not only wrong but also dangerous, trapping Israel in an illusion that is shattered time and again. ‘Control’ and ‘stability’ only exist between each inevitable round of violence. In fact, recurring rounds of violence are inherent to this approach.”

“’Conflict management’ means continued Israeli control over the Palestinians in Gaza and in the West Bank, with the inevitable reality of organizations and factions struggling to overthrow that control. Under the illusion that the conflict is being managed, opportunities for change provided by calm periods are squandered….” 

“So long as Hamas is willing to use terror against innocent Israeli civilians and so long as it refuses to recognize the State of Israel, it will not be a ‘partner’ for peace. But it could be partner to interest-based agreements requiring it to modify its behavior, as many academic and security experts claim. In fact, despite Netanyahu’s being the most vocal opponent of dialogue with Gazan terror organizations, it was he who reached two agreements with Hamas: the 2011 Shalit deal and the 2012 agreement that ended Operation Pillar of Defense…” 

“A long-term resolution with respect to Gaza requires changing its political predicament. The only sensible way of doing this is to establish a Palestinian state in the West Bank and Gaza, a state whose existence would be negotiated with the Palestine Liberation Organization under Abbas’s leadership. As part of a comprehensive political agreement, Hamas is very likely to agree to a long-term truce, as its representatives have repeatedly said.”

“In 1997, its founder and spiritual leader Ahmad Yassin suggested a thirty-year hudna (truce) with Israel. In 2006, one of its leaders, Mahmoud al-Zahar, proposed a ‘long-term hudna’. Earlier this year, Sheikh Hassan Yousef, a senior Hamas functionary in the West Bank, reiterated the organization’s willingness for a hudna and said the organization was willing to accept a peace agreement with Israel if a majority of Palestinians supported it. In 2010, in an interview with a Muslim Brotherhood daily circulated in Jordan, Hamas’s political leader Khaled Mashal expressed pragmatic views and willingness to reach an agreement with Israel. In late July, he [said] ‘We want peace without occupation, without settlements, without Judaization, without the siege’.”

“All these proposals were contingent on ending the Israeli occupation and establishing a Palestinian state within the 1967 borders. They received no response from Israel. Although a Palestinian state contradicts Netanyahu’s ideological commitments and conflicts with his own political interests, a state is clearly in Israel’s interest….”

“The historic conflict with the Palestinians will not be settled by a single agreement. Reconciliation between Israelis and Palestinians—overcoming decades of bloodshed and hatred—will require a long process of acceptance and forgiveness spanning years and probably decades. The armed conflict, however, can certainly be ended. Israel has already ended armed conflicts with several neighboring countries: with some, like Egypt and Jordan, it achieved comprehensive peace agreements; with others, it agreed to other kinds of accords.”

“An agreement can be reached with the Palestinians, too: the terms are known and the price is fixed. Whether it is reached or not is a matter of political will on the part of Israeli and Palestinian leaders. Unfortunately, Israel’s current leadership will do anything to avoid this choice, to the detriment of both peoples.”

“The war in Gaza is, fundamentally, not about tunnels and not against rockets. It is a war over the status quo. Netanyahu’s ‘conflict management’ is a euphemism for maintaining a status quo of settlement and occupation, allowing no progress. The Israeli opposition must distance itself from this hopeless conception and other countries need to reject it. Both must be done forcefully and before violence erupts once more, and force becomes the only option—yet again.”

The Criminals Who Poison Our Elections

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Anybody with the sense God gave a goose understands that Republican efforts to stamp out voter fraud are really an attempt to reduce the number of Democratic voters. Here’s what’s been happening in Georgia:

[The Republican] Secretary of State publicly accused the New Georgia Project in September of submitting fraudulent registration forms. A subsequent investigation found just 25 confirmed forgeries out of more than 85,000 forms—a fraud rate of about 3/100ths of 1 percent [in decimal terms, that’s a rate of 0.000294].

Meanwhile, a group of civil rights lawyers filed a lawsuit claiming that thousands of registration forms submitted this summer still haven’t been recorded in Georgia’s voter database, “nearly all of them belonging to people of color in the Democratic-leaning regions around Atlanta, Savannah and Columbus”. State and county officials, however, said they have already processed all of the applications sent to them by the October 6 registration deadline, and anyway, there is no state law that requires properly-submitted registrations to be processed by any particular date. A local judge has declined to intervene, citing a lack of proof that the registrations have gone missing.

Then there is this detailed report from Al Jazeera America:

Election officials in 27 states, most of them Republicans, have launched a program that threatens a massive purge of voters from the rolls. Millions, especially black, Hispanic and Asian-American voters, are at risk. Already, tens of thousands have been removed in at least one battleground state, and the numbers are expected to climb…

At the heart of this voter-roll scrub is the Interstate Crosscheck program, which has generated a master list of nearly 7 million names. Officials say that these names represent legions of fraudsters who are not only registered but have actually voted in two or more states in the same election — a felony punishable by 2 to 10 years in prison.

How does this Crosscheck program work? You can appear on the list as a suspected felon if your first and last name matches the first and last name of someone who voted in another state:

The actual lists show that not only are middle names commonly mismatched and suffix discrepancies ignored [such as Jr. or Sr.], even birthdates don’t seem to have been taken into account. Moreover, Crosscheck deliberately ignores Social Security mismatches, in the few instances when the numbers are even collected.

A statistical analysis revealed that African-Americans, Hispanics and Asian-Americans appear on the list much more often than their percentage of the population would indicate, while white Americans appear less often. The reason is that there is less variety in the names of certain ethnic groups, and among those groups are African-Americans, Hispanics and Asian-Americans, groups that all tend to vote for Democrats. (By the way, you can enter your own name at the Al Jazeera America site and see if you’re right to vote may be challenged.)

If you’ve watched enough Fox News, you might conclude that the hordes of Democrats who poison our elections by illegally voting in more than one state don’t use the same birthdates or Social Security numbers when they register to vote in this state and that, so why bother matching on those criteria?

Or you might infer that America does indeed have a criminal element bent on interfering with the electoral process. Unfortunately, the most crafty and dangerous members of this criminal conspiracy are Republican officials whose job it is to administer elections.

PS — Paul Krugman wrote an excellent column the other day called “Plutocrats Against Democracy”. I suggest reading the whole thing, which isn’t very long. It ends this way:

But now you understand why there’s so much furor on the right over the alleged but actually almost nonexistent problem of voter fraud, and so much support for voter ID laws that make it hard for the poor and even the working class to cast ballots. American politicians don’t dare say outright that only the wealthy should have political rights — at least not yet. But if you follow the currents of thought now prevalent on the political right to their logical conclusion, that’s where you end up.

The truth is that a lot of what’s going on in American politics is, at root, a fight between democracy and plutocracy.

Professor Krugman is an optimist. He thinks the plutocrats haven’t already won.