War is Politics by Other Means

What happened in the American war in Vietnam?

I am watching the lengthy PBS series on Vietnam, which facilitates a great deal of sober reflection. This dates me, but I recall (barely) the nightly body counts on TV, and the arguments with family about what was going on, both abroad and in the US in reaction to the war. I was too young to be particularly anti-war or pro-war, but I was very perplexed. The US was the greatest nation ever, had nuclear bombs and aircraft carriers, and had sent people to the moon. What power did this tiny country so far away have that we did not have?

The salve of time helps to clarify that we had lost this war long before it ended. Because, in the Clausewitzian dictum, war is politics by other means. The North Vietnamese had something that we didn't, which was an unassailable political position and ideology. They were in effective charge of much of the South, especially rural areas, for most of the war. The North Vietnamese had the double political distinction of military victory against the French, and of effective land reform against the landlords. In comparison, the South Vietnamese government was a bumbling, corrupt holdover from the French, which spent its time alienating the majority religion of the country, Buddhism, and keeping the landlords in power over the peasants of the countryside. Who was going to win this battle for hearts and minds?

Yes, North Vietnam was run by communists, and is still. But their propaganda and policies were effective to the mass of the population, in selling themselves as nationalists first and foremost- victors over the Japanese, the French, and later on the Americans too. Who would mess with that kind of record? Unfortunately, to put it in LBJ terms, we got into a pissing match with the North Vietnamese. No one wanted to "lose" South Vietnam, or let communism snatch one more country, or be the first president to lose a war. So it was our pride vs the North Vietnamese pride. Sadly, this did not translate into political support or governing competence in South Vietnam. Its government crumbled in our hands, and no amount of napalm was going to fix that.

We should at this point (that is to say, roughly 1963) have reframed the whole effort in Vietnam as one strictly in support of the South Vietnamese government. The US military is never going to win hearts and minds in foreign countries, not unless, as in World War 2, we have utterly destroyed those countries first and brought all their civilians to their knees in thankfullness for ridding them of their demented fascist government. Not conditions that come around very often, thankfully. The more time we spend somewhere, (say, Afghanistan, or Iraq), the worse it gets. The fact that the US had previously propped up the French position in Vietnam didn't help either. So all we can realistically do is support the native government (and even that may bring taints of colonialism and racism, rendering that support rather poisonous). And in this case, the government of South Vietnam was a mess, and should have been left to die on its own. That is what the politics dictated at the time, and the PBS series makes it clear that this was apparent to those who knew what was going on. They showed a great passage by an ex-soldier from the North, to the effect that, were it not for the US, the North would have taken Saigon by 1966.

It is instructive to compare our effort in Korea. North Korea tried to set up a Viet Cong-style insurgency in the South as well, but it was crushed by our client there, Syngman Rhee. North Korea tried to drape itself in the banner of anti-Japanese militancy, but that didn't play particularly, since the overwhelming US role in defeating Japan was so clear. South Korea instituted effective land reform in 1948 as well, which was key to dampening enthusiasm for communism. One might wonder why communism excites enthusiasm at all, but to landless peasants whose rent is half their crop, and who suffer countless other humiliations, it is a pretty easy sell, at least before the collectivization drive begins(!) So the political position of South Korea, destitute as it was, was far better than that of South Vietnam vs their respective northern antagonists. One might also add ancient cultural patterns, whereby modern Vietnam was created over the preceeding millenium by the gradual southward military expansion of the North Vietnamese, after they had successfully defended themselves against the Mongol and Chinese empires. 

Ho Chi Minh city, present day. Is this communism?

So, communism. Vietnam suffered terribly upon reunification due to a decade of doctrinaire communism, as if the aftermath of our brutal war hadn't been bad enough. After the wonderous dispensation of market-Leninism (!), begun in 1986, it is now a moderately prosperous but still one-party state with a miserable human rights record. Vietnam is reaping rewards from the US-China trade tensions as it becomes a top destination for low cost manufacturing. The US is its top export market. Its citizens have 1.4 cell phone subscriptions per capita, and its Gini coefficient is now similar to that of the US. Buddhism remains the leading religion, which, while confined to a state-run Sangha and political impotence, is relatively free otherwise. 

The US was right to be against communism. States like North Korea, Cuba, China and Vietnam show that communism, even after all the reforms and backtracking on Marxist theory, is antithetical to fundamental human freedoms, due to its Leninist / Stalinist greed for single party political control, which implies vast intrusion into all aspects of civic, social, and personal life. Russia is backsliding into that mindset, and we are right to stand once again with a friend in need, this time Ukraine, against its onslaught. But the new war just goes to show the critical importance of having a friend able to stand on its own feet, politically. Our military help would be pointless if Ukraine were a rotten state, with Russian insurgents and sympathizers, say, running 70% of the rural communities, and the central government pursuing vendettas against the Orthodox church instead of shoring up its support on all fronts.

Integral to the politics of warfare are economic factors like land reform and inequality. It was the corruption and steadfast lack of recognition of the peasant's plight that destroyed South Vietnam. The Viet Cong would not have been able to mount an insurgency were the peasants not desperate and open to well-honed propaganda based on economic equality / opportunity. Ruthless terrorism played a role, as it did for the Taliban. But the basic position of hopelessness versus an uncaring state and economic system was fatal. We are facing similar issues ourselves, as people in rural areas feel left behind and neglected, despite being the beneficiaries of such various and generous handouts from the state that would make welfare recipients blush. No matter- the US has become incredibly unequal and economically/socially stagnent, which is a recipe for populism and revolt, of which we recently had a taste. As inequality rises in China and Vietnam, will they face class-based revolt, driven by some new ideology of equality, fraternity, and liberty?

• Krugman on inequality.
• Photos of Vietnam.
• A green transition.
• A plague of bad plates.

Deep Inside the Ribosome Factory

Hundreds of processes are involved in cranking out ribosomes. One is carried out by an RNA helicase.

Our evolutionarily older molecules have been through a lot, and show the scars of billions of years of jury-rigging. The ribosome is among the oldest, and most ornately decorated, with dozens of extra proteins pasted around the outside, chemical modifications of its RNA and proteins, and a system of scaffolding and maturation factors. It even has its own organelle to develop in- the nucleolus. The nucleolus organizes spontaneously around the portions of the genome that encode the ribosomal RNA (rRNA), which are transcribed in prodigious amounts and whose products go through a lengthy maturation process.

To give an idea of the scale of all this, the ribosomal RNA is about five thousand nucleotides long, and about a hundred of these nucleotides are chemically altered by extra processes, all of which are highly unsual, at least versus normal messenger RNAs. At least three sites are cleaved during maturation, and seventy nine different proteins are added that join the mature structure. There are also over two hundred accessory proteins and seventy-six small RNAs that do not join the mature ribosome, but are needed to facilitate the various folding and chemical modifications during the construction process, which is all done in an ordered fashion. In a cell like yeast, two thousand ribosomes are assembled per minute, taking up a huge share of cellular resources. For example, the ribosomal proteins take up about sixty percent of the mRNA production machinery in a growing yeast cell.

Overview of ribosomal RNA maturation. 25S is the large subunit precursor rRNA segment, while 18S is the small subunit precursor. The ITS segments are intervening  portions that are clipped out of the original long RNA. The small subunit (orange) has a somewhat quicker maturation path than the large subunit (red). Shapes change extensively as the nascent RNAs get prodded and pulled into their final shapes, as if the nucleolus were a tiny little hair salon.

The two halves of the ribosome, the small and large subunits, are separately made and matured, (with all the various constituent and helper proteins being imported back from the cytoplasm to take up their places in these nascent structures) and then exported from the nucleolus out to nucleus and on to the cytoplasm, where some final maturation steps take place, including removal of any remaining accessory factors, Last comes a test run through a fake synthesis cycle without any mRNA or tRNA substrates, after which defective ribosomes are destroyed.

This system is truly daunting in its complexity, but obviously not complexity borne of design. Rather, it is borne of desperation, as bandaid after bandaid has been applied to produce the massive machine that currently sits at the heart of protein synthesis. It is a classic snowball effect, where items added to provide a modicum of extra stability, speed, or accuracy each reinforce the conservation of the core mechanism, making it increasingly impossible to create any radical change or redesign. Optimization in this case has been the enemy of efficiency, since the core of the enzyme, based on RNA, is so intrinsically inefficient.

Structure of the ribosome at an intermediate state, when helicase Spb4 (pink) is attached. All of the colored proteins, in fact, are modifier/accessory factors and are destined to fall off eventually. The ITS2 is the intervening sequence from the ribosomal RNA which has also not yet been cleaved and prised off the structure, but will be soon.

A recent paper sought to look at one small part of this byzantine construction process- where a helicase attaches and participates in one of the later steps as the nascent large ribosomal subunit exits from the nucleolus to the nucleoplasm. Helicases are enzymes that help nucleic acids unwind, (and rewind), which is just the kind of thing the ribosomal RNA so desperately needs as it wends its way from a linear RNA to the compact final structure. The authors use the new method of cryo-electron microscopy to obtain atomic structures of the large subunit in various stages of dress. One image, below, shows some detail about how helicase SPB4 (pink) holds on to one small segment of the ribosomal RNA, wrenches it apart, and thus enables its small structural transition.

Closer structure of Spb4, showing how it grips the ribosomal RNA, which is denoted by the high numbers, G1919 to G1948, based on the nucleotide positions. It is also an ATPase, which powers its helicase activities. RecA1 and RecA2 refer to proteins domains within Spb4 that are characteristic of helicase enzymes, as their "hands". CTD refers to the end of the protein, its carboxy-terminal domain.

The paper is a long-winded discussion of the many protein-protein contacts being made among these accessory factors,  which come on first, then next, then which force others off, etc. Their conclusions are shown below, as a sequence of states where, though at first glance nothing seems to have happened, the final state is quite different in detail from the state C coming in, not only in terms of the accessory proteins present, but also in the structure of the core ribosome. Only eight different proteins are in play here, so this is a tiny slice of the whole process. What is happening to the ribosomal RNA, the target of all this activity? They provide a rundown of some of Spb24's effects as follows, though a full appreciation of its role remains unclear:

The accommodation of the rRNA substrate between the two RecA-like domains induces bending and strand separation of the rRNA around the base of ES27, resulting in an alternate base-pairing of helices H62/H63/H63a compared to nucleoplasmic maturation intermediates and mature 60S subunits. This may explain why the rRNA area at the base of 25S domain IV initially appears to form stable duplexes, while it becomes more flexible and accessible for chemical modification in presence of Spb4, suggesting that the helicase disrupts this region upon its association. In addition to the catalytic domain, Spb4’s essential CTD appears significantly involved in inducing substrate RNA strand disruption and establishing this alternate conformation. In the obtained substrate- bound state, the first half of the CTD (aa 406-499) is tightly docked onto the C-terminal RecA- like domain (RecA2) and binds H62/H63 nucleotides A1936 to C1941, thereby maintaining separation of the rRNA strands. Furthermore, a conserved tryptophan (W536) within the flexible C-terminal tail of the CTD (aa 500-606) intercalates between nucleotides of the immature H62/H63/H63a rRNA, which later adopts its mature-like fold in nucleoplasmic pre-60S particles. - Authors; (ES27 denotes a region of the ribosomal RNA near the active site, as does domain IV. H62/63 denote helices of rRNA, as shown in the diagram above.)

 

Schematic of what is happening to the large ribosomal subunit during these few steps. Accessory factors by the dozens are coming and falling off as the whole process happens, while also guiding the ribosome through its transport process from nucleolus out to the cytoplasm, while in addition doing various QC steps that can shunt defective complexes to cellular waste bins.

• Thelonious.
• All about reading.

Prisons as Social Prisms, Mirrors, and Shadows

From deTocqueville to BLM by way of Solzhenitsyn.

Carl Jung promoted the concept of the psychological shadow- that part of ourselves that is dark, bad, and repressed. It tends to be what we project on others, leading to the kind of political and cultural polarization we see so much of today. For individuals, integrating the shadow, (that is, at least perceiving it, if not valuing it), is difficult but an important path to a more mature and integrated self. Societies have similar psychological characteristics, and have shadows that they project on others, both other cultures and unfortunate classes in their own system. Unlike shadow elements in individual psychology, which are all too easily hidden and ignored, people are harder to keep out of sight, so societies do a lot of explicit work to heap opprobrium on the lower classes- minorities and the poor, in a social process that keeps the social hierarchy stable, and keeps the majority self-satisfied.

A big product of the shadow work of society has appeared in prisons. In primitive times, no one had prisons, and criminals were tortured, killed or ostracized. Now, the world is too small, ethical standards have risen somewhat, and we have turned to prisons as a general purpose punishment- a modern form of ostracism. Prisons express (and contain) our attitudes and definitions of antisocial activity and contagion. Alexis de Toqueville came to the early US to investigate our prisons, as a way of gaining insight into our society, before being waylaid into a much more general tour of this vibrant country. But his instincts were sound. France had been through its revolution only forty years prior, with its gruesome imprisonments and executions, which mirrored the tumultuous reversals of the social order. In the US, de Toqueville found a relatively unsophisticated and small carceral system, as money was short and there was plenty of room for criminals to disappear out west. It did not turn out to be an interesting prism on American life.

Today things are vastly different. The gangster era of the 20's and 30's led to a new focus on crime, noir, and high-profile prisoners like Al Capone. The crime and drug era of the 80's and 90's led to an almost four-fold increase in the prison population, so that now the US leads the world with a prison population of roughly 0.5% of the population behind bars. The BLM movement and defund the police movements were in part about recognizing that something had gone serious astray here. Whether it originated from environmental lead poisoning, or social breakdown, or drug cartels, the result was a huge population of ostracized, mostly male, and disproportionately minority people locked away. On top of that, the society had lost interest in rehabilitation amidst its turn to more conservative attitudes that valorize the rich and powerful and disparage the poor and disadvantaged. 

Our prisons today say alot about us as a society. Not that prisons are not needed, and that there aren't true criminals and insidious criminal organizations that prey on the rest of society; but our lack of empathy and lack of a wider social vision is palpable. Particularly, our attachment to property, its "rights", its local and parochial control, and particularly its inheritance, has gotten a little extreme. It is the perpetuation of privileges through property and wealth that explain a lot of the persistent lack of social mobility, the vast industries of greed/tax avoidance, easily politicized fears. Capitalism is at its heart competitive, and having winners of billions implies also having losers- those who sleep on the street, and those locked up, not to mention the hordes of low-wage workers who make everything go.

All this came to mind as I read Aleksandr Solzhenitsyn's Gulag Archipelago. It is a vast tome, befitting the vast archipelago it describes, its huge population, its protracted duration, its unimaginable suffering, and what it says about its society. While unexpectedly enjoyable to read, as Solzhenitsyn is joking the whole time in various sarcastic and dark modes, it is an indictment of Soviet Russia on a comprehensive basis. One particularly striking theme that he weaves through is comparison with the Tsarist period that came before. Solzhenitsyn meets prisoners, often dedicated socialist revolutionaries, who had done time under the Tsar, and regarded that experience as heaven compared to what they were faced with now, under Stalin. To put it very bluntly, Russia used to be a civilized country. Now, under the Bolsheviks, torture of the most vile kinds is practiced, less vile kinds are routine, execution is carried out on a whim, and law and justice are a mockery. The Gulag is loaded up with many orders of magnitude more political prisoners than the Tsar had ever contemplated and works them mercilessly to early graves.

Breaking rocks in the gulag.

While this all mostly reflected the paranoia and totalitarian genius of Stalin, he was only following his model, Lenin, as Solzhenitsyn lays out in particularly damning detail. The larger Russian society clearly had, and still has, an ambivilent nature, as close students and subjects of the Mongols, but also as eager to engage with and learn from Western Europe. Who knew that the most left-tinged and idealistic ideology to be imported from the West would so quickly curdle into a second coming of Ivan the terrible? But so it did, and Solzhenitsyn describes what that really meant in human suffering, in this book that may have done more than any other to delegitimize and ultimately destroy that system.

• The neighborhood to prison pipeline in the US.
• The questionable science of ice cream.
  

Molecules That See

Being trans is OK: retinal and the first event of vision.

Our vision is incredible. If I was not looking right now and experiencing it myself, it would be unbelievable that a biological system made up of motley molecules could accomplish the speed, acuity and color that our visual system provides. It was certainly a sticking point for creationists, who found (and perhaps still find) it incredible that nature alone can explain it, not to mention its genesis out of the mists of evolutionary time. But science has been plugging away, filling in the details of the pathway, which so far appear to arise by natural means. Where consciousness fits in has yet to be figured out, but everything else is increasingly well-accounted. 

It all starts in the eye, which has a curiously backward sheet of tissue at the back- the retina. Its nerves and blood vessels are on the surface, and after light gets through those, it hits the photoreceptor cells at the rear. These photoreceptor cells come in two types, rods (non-color sensitive) and cones (sensitive to either red, green, or blue). The photoreceptor cells have a highly polarized and complicated structure, where photosensitive pigments are bottom-most in a dense stack of membranes. Above these is a segment where the mitochondria reside, which provide power, as vision needs a lot of energy. Above these is the nucleus of the cell (the brains of the operation) and top-most is the synaptic output to the rest of the nervous system- to those nerves that network on the outside of the retina. 

A single photoreceptor cell, with the outer segment at the very back of the retina, and other elements in front.

Facing the photoreceptor membranes at the bottom of the retina is the retinal pigment epithelium, which is black with melanin. This is finally where light stops, and it also has very important functions in supporting the photoreceptor cells by buffering their ionic, metabolic, and immune environment, and phagocytosing and digesting photoreceptor membranes as they get photo-oxidized, damaged, and sloughed off. Finally, inside the photoreceptor cells are the pigment membranes, which harbor the photo-sensitive protein rhodopsin, which in turn hosts the sensing pigment, retinal. Retinal is a vitamin A-derived long-chain molecule that is bound inside rhodopsin or within other opsins which respectively confer slightly shifted color sensitivity. 

These opsins transform the tickle that retinal receives from a photon into a conformational change that they, as GPCRs (G-protein coupled receptors), transmit to G-proteins, called transducin. For each photon coming in, about 50 transducin molecules are activated. Each of activated transducin G-protein alpha subunits induce (in its target cGMP phosphodisterase) about 1000 cGMP molecules to be consumed. The local drop in cGMP concentration then closes the cGMP-gated cation channels in the photoreceptor cell membrane, which starts the electrical impulse that travels out to the synapse and nervous system. This amplification series provides the exquisite sensitivity that allows single photons to be detected by the system, along with the high density of the retinal/opsin molecules packed into the photoreceptor membranes.

Retinal, used in all photoreceptor cell types. Light causes the cis-form to kick over to the trans form, which is more stable.

The central position of retinal has long been understood, as has the key transition that a photon induces, from cis-retinal to all-trans retinal. Cis-retinal has a kink in the middle, where its double bond in the center of the fatty chain forms a "C" instead of a "W", swinging around the 3-carbon end of the chain. All-trans retinal is a sort of default state, while the cis-structure is the "cocked" state- stable but susceptible to triggering by light. Interestingly, retinal can not be reset to the cis-state while still in the opsin protein. It has to be extracted, sent off to a series of at least three different enzymes to be re-cocked. It is alarming, really, to consider the complexity of all this.

A recent paper (review) provided the first look at what actually happens to retinal at the moment of activation. This is, understandably, a very fast process, and femtosecond x-ray analysis needed to be brought in to look at it. Not only that, but as described above, once retinal flips from the dark to the light-activated state, it never reverses by itself. So every molecule or crystal used in the analysis can only be used once- no second looks are possible. The authors used a spray-crystallography system where protein crystals suspended in liquid were shot into a super-fine and fast X-ray beam, just after passing by an optical laser that activated the retinal. Computers are now helpful enough that the diffractions from these passing crystals, thrown off in all directions, can be usefully collected. In the past, crystals were painstakingly positioned on goniometers at the center of large detectors, and other issues predominated, such as how to keep such crystals cold for chemical stability. The question here was what happens in the femto- and pico-seconds after optical light absorption by retinal, ensconced in its (temporary) rhodopsin protein home.

Soon after activation, at one picosecond, retinal has squirmed around, altering many contacts with its protein. The trans (dark) conformation is shown in red, while the just-activated form is in yellow. The PSB site on the far end of the fatty chain (right) is secured against the rhodopsin host, as is the retinal ring (left side), leaving the middle of the molecule to convey most of the shape change, a bit like a bicycle pedal.

And what happens? As expected, the retinal molecule twists from cis to trans, causing the protein contacts to shift. The retinal shift happens by 200 femtoseconds, and the knock-on effects through the protein are finished by 100 picoseconds. It all makes a nanosecond seem impossibly long! As imaged above, the shape shift of retinal changes a series of contacts it has with the rhodopsin protein, inducing it to change shape as well. The two ends of the retinal molecule seem to be relatively tacked down, leaving the middle, where the shape change happens, to do most of the work. 

"One picosecond after light activation, rhodopsin has reached the red-shifted Batho-Rh intermediate. Already by this early stage of activation, the twisted retinal is freed from many of its interactions with the binding pocket while structural perturbations radiate away as a transient anisotropic breathing motion that is almost entirely decayed by 100 ps. Other subtle and transient structural rearrangements within the protein arise in important regions for GPCR activation and bear similarities to those observed by TR-SFX during photoactivation of seven-TM helix retinal-binding proteins from bacteria and archaea."

All this speed is naturally lost in the later phases, which take many milliseconds to send signals to the brain, discern movement and shape, to identify objects in the scene, and do all the other processing needed before consciousness can make any sense of it. But it is nice to know how elegant and uniform the opening scene in this drama is.

• Down with lead.
• Medicare advantage, cont.
• Ukraine, cont.
• What the heck is going on in Wisconsin?
• Graph of the week- world power needs from solar, modeled to 2050. We are only scratching the surface so far.

Consciousness and the Secret Life of Plants

Could plants be conscious? What are the limits of consciousness and pain? 

Scientific American recently reviewed a book titled "Planta Sapiens". The title gives it all away, and the review was quite positive, with statements like: 

"Our senses can not grasp the rich communicative world of plants. We therefore lack language to describe the 'intelligence' of a root tip in conversation with the microbial life of the soil or the 'cognition' that emerges when chemical whispers ripple through a lacework of leaf cells."

This is provocative indeed! What if plants really do have a secret life and suffer pain with our every bite and swing of the scythe? What of our vaunted morals and ethics then?

I am afraid that I take a skeptical view of this kind of thing, so let's go through some of the aspects of consciousness, and ask how widespread it really is. One traditional view, from the ur-scientific types like Descartes, is that only humans have consciousness, and all other creatures, have at best a mechanism, unfeeling and mechanical, that may look like consciousness, but isn't. This, continued in a sense by B. F. Skinner in the 20th century, is a statement from ignorance. We can not fully communicate with animals, so we can not really participate in what looks like their consciousness, so let's just ignore it. This position has the added dividend of supporting our unethical treatment of animals, which was an enormous convenience, and remains the core position of capitalism generally, regarding farm animals (though its view of humans is hardly more generous).

Well, this view is totally untenable, from our experience of animals, our ability to indeed communicate with them to various degrees, to see them dreaming, not to mention from an evolutionary standpoint. Our consciousness did not arise from nothing, after all. So I think we can agree that mammals can all be included in the community of conscious fellow-beings on the planet. It is clear that the range of conscious pre-occupations can vary tremendously, but whenever we have looked at the workings of memory, attention, vision, and other components assumed to be part of or contributors to conscious awareness, they all exist in mammals, at least. 

But what about other animals like insects, jellyfish, or bacteria? Here we will need a deeper look at the principles in play. As far as we understand it, consciousness is an activity that binds various senses and models of the world into an experience. It should be distinguished from responsiveness to stimuli. A thermostat is responsive. A bacterium is responsive. That does not constitute consciousness. Bacteria are highly responsive to chemical gradients in their environment, to food sources, to the pheromones of fellow bacteria. They appear to have some amount of sensibility and will. But we can not say that they have experience in the sense of a conscious experience, even if they integrate a lot of stimuli into a holistic and sensitive approach to their environment. 

The same is true of our own cells, naturally. They also are highly responsive on an individual basis, working hard to figure out what the bloodstream is bringing them in terms of food, immune signals, pathogens, etc. Could each of our cells be conscious? I would doubt it, because their responsiveness is mechanistic, rather than being an independent as well as integrated model of their world. Simlarly, if we are under anaesthesia and a surgeon cuts off a leg, is that leg conscious? It has countless nerve cells, and sensory apparatus, but it does not represent anything about its world. It rather is built to send all these signals to a modeling system elsewhere, i.e. our brain, which is where consciousness happens, and where (conscious) pain happens as well.

So I think the bottom line is that consciousness is rather widely shared as a property of brains, thus of organisms with brains, which were devised over evolutionary time to provide the kind of integrated experience that a neural net can not supply. Jellyfish, for instance, have neural nets that feel pain, respond to food and mates, and swim exquisitely. They are highly responsive, but, I would argue, not conscious. On the other hand, insects have brains and would count as conscious, even though their level of consciousness might be very primitive. Honey bees map out their world, navigate about, select the delicacies they want from plants, and go home to a highly organized hive. They also remember experiences and learn from them.

This all makes it highly unlikely that consciousness is present in quantum phenomena, in rocks, in bacteria, or in plants. They just do not have the machinery it takes to feel something as an integrated and meaningful experience. Where exactly the line is between highly responsive and conscious is probably not sharply defined. There are brains that are exceedingly small, and neural nets that are very rich. But it is also clear that it doesn't take consciousness to experience pain or try to avoid it, (which plants, bacteria, and jellyfish all do). Where is the limit of ethical care, if our criterion shifts from consciousness to pain? Wasn't our amputated leg in pain after the operation above, and didn't we callously ignore its feelings? 

I would suggest that the limit remains that of consciousness, not that of responsiveness to pain. Pain is not problematic because of a reflex reaction. The doctor can tap our knee as often as he wants, perhaps causing pain to our tendon, but not to our consciousness. Pain is problematic because of suffering, which is a conscious construct built around memory, expectations, and models of how things "should" be. While one can easily see that a plant might have certain positive (light, air, water) and negative (herbivores, fungi) stimuli that shape its intrinsic responses to the environment, these are all reflexive, not reflective, and so do not appear (to an admittedly biased observer) to constitute suffering that rises to ethical consideration.