# Open Email: Perception, Memories, and the Paradox of Time

## Preamble

#### Steve Bond

Imagine something. No, seriously, close your eyes for a second, and imagine anything you like. I’ll wait.

Your brain contains on the order of 100 billion neurons, with each neuron making somewhere between tens and tens-of-thousands of connections with other neurons. This adds up to an estimated 100 trillion neuronal connections, and that little day dream you just enjoyed probably tickled about a billion of them. Now comes the hard part: Ask yourself if that daydream was somehow ‘more’ than the sum of a million neurons passing around a billion little handshakes. I bet it feels like ‘more’ to you, but you’d be wrong.

The brain is a living computer, and every memory; every emotion; every sensation; is a circuit that was initially executed because of some input, then strengthened because it was used. But again, the brain is a living computer, and unlike its silicon counterpart, the circuits are not fixed in place. While a given memory may always seem the same to the person experiencing it, the circuit is constantly rewiring itself, sometimes in pretty fundamental ways. Memories are these plastic things, and perception is bound inseparably to them. Please forgive me as I lapse into this existential black hole, but from the time we are born until briefly later when we die, everything that is ‘us’ is contained in some thousands or millions of these little circuits in a few kilos of undulated tissue — and ‘us’ is never standing still. Every day we perceive the world a little differently, and frankly, I think that’s pretty amazing.

Which brings me to my point; my good friend Sorin is a computer engineer with a propensity for philosophical musings about the human condition. In a recent email, he speculated about how opinions are formed, how ‘behavioural heuristics’ may make it difficult to identify (and possibly alter) personal character traits, and how the perception of time can be very different among individuals and cultures. This discussion was stimulated by a recent article in NewScientist, where Clare Wilson set out to understand what a memory actually is. Spoiler alert: It’s neurons making connections 😉

So, without further adieu, I bring you the second installment of Garbargal’s experiment in public email.

## On Perception, Memories, and the Paradox of Time

#### Sorin Alexander

Steve,

I just finished reading a book on conflict resolution in areas of protracted violence and the concept of time came up as being a huge area of misunderstanding between western/modern and tribal/native points of view. This article shed some light on why, from the point of view of memory formation and recollection, the past history or “narrative” of a people plays such a huge role in both the present and the future and should be considered during peace negotiations. In other words, the contemporary motto of “forgive and forget” simply does not work and ignores, after reading [the NewScientist] article, the fundamental way in which we store memories as well as how we imagine the future – which are linked, surprisingly.

Topics related to human behavior have fascinated me for some time – in fact they are more interesting to me than most other topics. I have discovered that I can apply some of the same techniques in figuring out certain behavioural aspects as I would in determining how to solve a computer science problem, for example. This is simply because I am, at the end of the day, trained to be an engineer and I can relate to the practical and application aspect of theory much more readily. Root-cause analysis has helped me identify behavioural patterns in myself and, if I so desired, allowed me to change them. However, in many cases of behavioural heuristics, such an approach is difficult and one must rely on what I refer to as “fluffy science”. This is because, while there are many fascinating experiments focused on how people will behave under various conditions and biases (often counter-intuitively or non-optimally, btw), there is often no good explanation as to why such behavior takes place. One ends up forming opinions based on feelings or instinct. This is the reason why concrete results such as the ones presented in the mentioned article are so fascinating to me. In this case there was a real example of how the fluffy science of the way different cultures view time can be explained in terms of concrete brain functions.

The topic remains on the edge of pure science and blends with intuition and observation of human behavior. If you feel that the forum you mention can handle such discussions, it’d be fascinating for me to participate. I have not read the full transcript of the electro-magnetic waves discussion but it seems quite a bit more in line with what I call hard science than the behavioural “fluffy” science I brought up.

And to give you an example of why this topic would be different, let me try to describe the time paradox I allude to above. Many cultures will, when talking about what we refer to as the past, allude to it being in front of us. The future, conversely, is behind us. They talk about the past that lies ahead. Concepts such as “living memory” or “remembered history” or “personal immortality” are hard to describe scientifically but they play real roles in how people perceive time and space (and who they are). Even if we had a grasp of what these concepts really refer to, one cannot come up with a formula or prescriptive method of determining what these ideas will mean to different people. It’s because of this that these concepts are often ignored during negotiations. So the “human” aspect is extremely relevant here while the hard science is often lacking. And there is the obvious temptation to invoke unseen hands pulling unseen strings…

PS. The best way to imagine the time paradox I mention (from my point of view) is the following. The past is all we know. The future we cannot see. We can only see what is in front of us – the past. The future, therefore, lies behind us. We walk backwards into the future. Or the future flows towards us from behind. Furthermore, there are metaphysical concepts of circular time sprinkled all over. Fascinating, no? 🙂

#### Steve Bond

Hey Sorin,

Although it’s pretty removed from my area of expertise, I see no reason why perception can’t be studied rigorously. If we start from the premise that all perception is linked to the activity of a finite number of cells in the brain, then it just comes down to the resolution at which we can measure that activity. While we don’t currently have the technology to monitor all the going-ons in a complete human brain, or model one in silico, I’m unaware of any fundamental constraint that would prevent us from developing the technology eventually. Even without futuristic advancements, a lot can be learned from properly controlled experiments; these can range from direct biological manipulation to sociological surveys. Some really interesting work has been done on colour perception that opens the door to answering the question ‘is colour a personal experience’ (i.e., do we both see fire trucks and stop signs as red, but your red is my blue)? When red-sensitive photoreceptors were introduced into the retina of monkeys (they usually work on a blue/yellow colour wheel, similar to human red-green colour blindness), they were able to make sense of that new information (Mancuso et al., 2009). There’s a company working towards a new gene therapy to treat humans with colour blindness, and I’m going to make a prediction that when they start asking these patients “what colour is ‘red’ most similar to”, they are going to give different answers. What I’m really excited about, however, is the potential to give us ‘normal’ sighted people new photoreceptors for UV light. I’d sign up for the ability to see more like a chicken 😉

I also wonder if what you are labelling as ‘fluffy science’ would be better broken up into two different categories. The first being intuition, which isn’t really sciency at all, and the second being philosophy. With respect to time perception, I feel fully justified in commenting from the position of the first category. I experience the relentless march of time, in its linear forward direction, therefore it must be! All this talk of the future laying behind us must be bogus, and is probably sufficient to declare war over. From a philosophical perspective, reasoned from well excepted first principles, I’m falling short. Other people seem to have thought deeply about it though. As for rigorous science, just last month a case study was released of two women who suffered from a rare form of encephalitis (Kuroda et al., 2015). They experienced an ‘autobiographical age awareness disturbance’, where much older memories overrode more recent memories, leading them to believe they were living in the past. By monitoring brain activity and carefully tailoring their interview, the researchers are able to build a case for how the brain constructs a linear narrative of perceived time. This is the type of work that will continually peel away our need to rely on intuition, and hopefully we will be able to collectively train ourselves, as a society, to make important decisions based on facts instead of emotion. Maybe the time will come when negotiators will quite literally hook themselves up to brain scanners to ensure everyone is on the same page before they begin!

-Steve

#### Vinai Bhagirath

Sorry this took so long. I’ve been thinking about this off and on since the original post, and actually drafted something that I later deleted because it wasn’t really relevant. This is more of a meditation that an investigation, since I don’t think there’s a clear question we’re trying to answer, but rather simply thinking about an interesting topic.

There are a few points I’d like to make:

1. Because of the way our bodies are structured, we tend to think of “thought” as words and images. But we should remember that all brain activity is more similar than different. So, a lot of activity is going on that isn’t explicitly attended to (that is, we don’t usually pay attention to it, sometimes are incapable of paying attention to it). For example, riding a bicycle requires memory and cognition, but could be done by someone who is incapable of identifying a bicycle or speaking or understanding words (e.g. because of brain injury). And the brain function that regulates your heart rate or digestive processes is not fundamentally different than the processes that result in images or narrative memories. The reason I bring this up is to further illustrate the point that there is nothing “special” about imagining, memory, language, etc. except that these are more complex. And to those that marvel at the emergent properties of complex systems, I would argue they are not fundamentally impressive, but seem so to humans precisely because they are occurring at the same scale as our processing system. If we had a vastly more complex and capable cognitive system, we would look on symphonies etc. as facile, and the things that are wonderful to us now would be simple and perhaps uninteresting.
2. Steve, you commented that a thought is a pattern of neuronal connections and activity. I think those of us reading this will agree that, clearly, cognition is mainly a function of the brain. But it’s important to remember that the brain is not separate from the rest of the body. Most obviously, perception occurs via various organs and perception is integral to thought. So, you may feel something with your hand, and this stimulus will interact with your brain in a way that is not fundamentally different than the way a memory would interact with your thinking. If someone cuts out your thyroid gland, your cognition will unavoidably be affected. Which is just to point out that, strictly speaking, your brain doesn’t produce thoughts in isolation. And, if we take this point further, the environment also interacts with the body and brain tissue to influence thought. So, although it is obvious, it’s important to remember that cognition is a product of the entire system. See below why I think it is important to remember.
3. Sorin, I think that one of the concepts you find interesting is that our cognition can result in behaviours that are apparently at odds with our desires or goals. But the difficulty is in defining those goals. People are perfectly capable of desiring things which are mutually exclusive or diametrically opposed. I think, before getting into details of cognitive processes, there’s a lot that could come from simply asking people to think carefully about, define, and make explicit their values and goals. The reason I bring this up is because we judge cognition and other processes mainly by their ability to attain a goal. So, we decide whether someone is thinking “clearly”, “correctly”, “properly”, or even “differently” mainly by the effect of the thinking on the ability to achieve some end. This is why things get “fuzzy”. People have conflicting goals and values, and parsing them requires processes that acknowledge and allow for this.

People are studying the neurobiology of addiction (to substances or behaviours), for example. They are sorting out the neuronal pathways that are involved, and how substances of abuse can alter them. But they are also examining the ways these pathways sometimes include extracorporeal elements; for example, it is well known that certain environmental or social cues can reinforce nicotine addiction, and if they are removed, the addiction is less powerful. That would be the person who takes breaks at work with smoking colleagues, and cannot quit so long as he continues this behaviour. And if someone really valued smoking, and really desired to smoke given a full understanding of the net effect, then the addiction would be irrelevant and we would simply call this a choice or preference.

Better send this off without further thought or no one else will ever see it! I was looking at some neurobiology reviews and will let you know if I find anything of general interest.

-Vinai

# Open Email: Waves and Transparency

## Preamble

#### Steve Bond

In the winter-spring of 1999 I was one of the fortunate few attending the Ontario Science Center Science School; a semester long program for senior high school students who really dig science. Participants take on a normal-ish course load of science and math classes that cover all core curriculum, with added awesomeness like access to high end laboratory resources and a lot of flexibility/support when designing independent research projects. Did I mention this was all taking place inside the Ontario Science Center? Super cool.

While the freedom and toys were all very nice, the greatest value was in the incredible people. Maybe your experience was different from mine but I’ll estimate that only 15-20% of my home-school (not to be confused with home-schooled) classmates actually cared much about the learning aspect of high school. This was fine, because whatever, but then I found myself in this magical wonderland where everyone cared. And I’m not talking about marks driven, stressed out, helicopter parent pressure, ‘I’m 18 and don’t know what I’m doing with my life’, type caring; I’m talking about the-world-is-marvelous-and-holy-shit-I-get-to-live-in-it, type of caring. I really, really, liked these people.

I like the idea of using a blog as a place for discussions; open email, for content that may have some broader interest. An experiment in public discourse by some old friends from Science School.

## On Waves and Transparency

#### Vinai Bhagirath

Dear Steve,

Just following up on a question that came up when you were visiting. If I remember correctly, something like, “Why can radio waves penetrate solid objects?” I thought it was something about diffracting through tiny gaps in doors, etc. That was close, but wrong.

15 minutes of Internet surfing has led me to the following explanation, which is probably somewhere close to being consistent with reality.

Why is matter sometimes transparent to waves? Essentially, matter is transparent to waves under two conditions: 1) when it does not interact with the wave; 2) when it does, but it interacts in such a way that the direction of the wave’s propagation is not changed (i.e. there is little “scatter”).

1) Electromagnetic waves can interact with electrons in matter. I don’t know all the determinants of the likelihood that a wave will interact with an electron (one will be density of the matter), but if the energy of the wave is similar to an amount of energy that can be absorbed by the electron, say to jump a shell, then there can be an interaction. If you have very high energy waves, like gamma waves, then they can pass through matter, only occasionally ionizing an electron, since it’s too high energy for a common shell-jump. (This is kind of unsatisfying: why is a shell-jump more likely than an ionization? Because high-frequency waves are “small”? Maybe this is leading down the quantum mechanics rabbit hole…) If you have a low energy wave (radio wave) then it’s less likely to be the “right” energy for an electron. The electrons of conducting materials are particularly susceptible to interaction with electromagnetism (what does that even mean, “particularly susceptible”?), which is why many conductors such as metals are opaque to a wide range of frequencies. I think that elements with large nuclei are more opaque to electromagnetism because there is more likelihood that the wave will interact with the nucleus. I think if you have a very non-dense gas, then the wave is unlikely to interact with it because there is little to interact with. But there is another way in which materials are transparent (see below) and I’m not sure which predominates in gases. But this section (1) gives a rough idea of why a wooden wall is transparent to gamma waves, but not visible light or infrared, and gives one of the reasons why wood is transparent to radio waves.

2) Apparently, if you put a stick in water which has waves passing through it, the wave will diffract around the stick and you will scatter the direction of the wave. I guess this happens with molecules and electromagnetic waves, too, since X-ray crystallography is a real thing. If you place many sticks at a recurring distance that is close to or smaller than the wavelength in the water, the diffracting waves will tend to destructively interfere, whereas this doesn’t happen in the “forward/backward” dimension, so the wave propagates through. Since molecules of fluids tend to be jostled tightly together, the size of the waves that are transmitted in this way includes visible light. Which is why lead glass is a real thing that is opaque to gamma rays (phenomenon 1) but transparent to visible light (phenomenon 2). If the material has electrons which can jump levels at energies that are in the visible spectrum, then it will appear to have a colour, although the rest of the light will pass through without scattering. This would be the case for Kool-Aid, or urine.

Since radio waves are very large, phenomenon 2) occurs with solids and they propagate through without scattering. Since they are low-energy, phenomenon 1) also occurs, I think. But, materials whose electrons can interact with low-energy waves, like conductors whose electrons are very promiscuous, will be opaque to radio waves. So you will not be able to listen to the radio in a room whose walls are made of gold (or iron, or tin, or silver). But you can listen to the radio in a room whose walls are made of solid brick or wood. Apparently, small changes in the conductivity of the walls, such as when they are wet, can make a big difference in opacity to radio waves, which may be part of the reason reception is poorer when it’s raining.

Also, phenomenon 2) causes a brick to be opaque, and phenomenon 1) causes it to be red. And mirrors work by phenomenon 2) except that the wave is propagated backwards instead of forwards. I think that is why water and glass are mirrors.

As usual, it’s all a matter of putting it in metaphors to help us remember what actually happens. The more I read what I’ve written, the less satisfying it is. Would appreciate a physicist’s input on the following:

1.  how does lead glass work (absorbs gamma, but transmits visible)? This may be another way of asking why are gamma waves more susceptible to interaction with nuclei than visible light waves?
2. why does the sky appear blue? (and please explain what you mean by “scatter” when answering this question, and how “scatter” results in a blue appearance.)

#### Vina Bhagirath

OK. Figured out why the sky is blue. Essentially, because our brains rely on rectilinear propagation of light. Since the wavelength of blue light is shorter than that of red light, the spaces between molecules of air are more likely to be farther apart than the wavelength of blue light. Since the canceling out thing happens best when the spaces are smaller than the wavelength, there is less canceling and more scattering of blue light. Light from the sun is going in all directions, including off to the right and left of our eyes. If this blue light is scattered to our eye, our brain assumes it originated from some point in the sky to the right or left of the sun. This is true for all the points around the sun, so we see the sky as blue.

I’d be more happy if I could be shown that the distance between air molecules is right for this to work. Could probably do a napkin calculation… AND, I’m going to try the sticks in water thing. Which would be better with people in a wave pool…

For the sky being blue: it is due to Rayleigh scattering, or scattering of light off particles significantly smaller than the wavelength. This obtains in our atmosphere: visible light has a wavelength of ~500 nm and a nitrogen molecule is ~50 pm. The probability that a photon will Rayleigh scatter is proportional to the “cross-section” of the molecule, but cross-section is just a synonym for this same probability, and it is wavelength dependent—in fact, strongly wavelength dependent:

σ ∝ l / λ4

where l is the size of the particle and λ is the wavelength. So shorter wavelength scatters much more efficiently than longer wavelengths—hence, more blue light is scattered by molecules in the sky towards you. This is also why the sun is yellow-red in colour: the blue has been scattered away; and at sunset, the amount of atmosphere is great enough that the blue gets scattered away from the surrounding atmosphere making it red or orange.

So at the end of the day, it doesn’t have anything to do with the spacing of the molecules in the sky, but only with the fact that they are small compared to a wavelength of light. The rest of the effect is driven by the various wavelengths of visible light.

As for the question of how transparent stuff is to various types of waves, I think some of the basics are correct. For electromagnetic interaction, though, I believe it doesn’t have much to do with exciting transitions between atomic energy levels. It has more to do with interaction with free electrons or electrons in the outer shell that aren’t strongly localised to a particular atom. In a solid, it isn’t as though every electron belongs to a specific nucleus. And it’s the wave interacting with these free or semi-free electrons that makes the difference. Peter can probably speak to this a lot better than I can. Astrophysics is mainly about gases and plasmas and solid state physics is more subtle!

For a mirror, though, I think it’s pretty easy to get a mental cartoon of what’s going on. The light excites free electrons at the surface of the conductor and they begin oscillating at the same frequency as the light. But because accelerating charges radiate light, the oscillating electrons re-radiate the same wavelength that they absorb.

#### Peter Hitchcock

Well, I’ve been thinking and reading about this for the past few days (and asking my dad) because I don’t feel very satisfied with the answers that I have. This being said, I think that there are some problems with the metaphors you put forward, Vinai. (This is always the case – to paraphrase, all metaphors are wrong, some are useful.)

One shift in perspective for me over the past days that I think is important is that the question is the wrong way around: we shouldn’t ask why solid (or indeed any) matter is transparent, but rather why any matter is opaque. We see EM waves, which are produced by accelerations of charged particles. ‘Solid’ objects aren’t opaque by default – they are opaque because some process absorbs or scatters incident EM waves.

The second thing to say is that both the EM waves and the atoms they interact with are quantum phenomena, but their quantum nature becomes more obvious in certain limits. For some processes classical metaphors work well for the radiation, for others you need quantum ideas, and a similar divide exists for the electrons/atoms, though there are some fundamental quantum things you can’t really get away from in the latter case. So rather different metaphors are useful for Rayleigh scattering than for compton scattering of gamma rays.

The most useful classical rule of thumb is that waves interact with structures that have length scales similar to their wavelength. This is true of all waves, not just EM radiation; for instance, to think about the water waves Vinai appealed to, if the stick is much smaller than the wave, it’s not much different from just raising and lowering the level of the water around the stick. If the stick is much bigger than the wave, the wave will reflect off of it geometrically in much the same way light bounces off a mirror, or sound off of a wall. If the length scales are comparable, you get complicated patterns of constructive and destructive interference that depend a lot on the scattering direction

Ok, so if we’re talking about visible light (wavelength say about 500 nm), atoms and small molecules are way smaller, so they don’t interact very strongly. Rayleigh scattering happens because the electric field associated with the wave will tend to push electrons and protons in opposite directions, though it’s like pulling against a stiff spring. Nonetheless, you are accelerating charged particles, and you get weak emission of photons at the same frequency as the incident light, and the directional dependence of the scattering is pretty simple. It gets much stronger (as Adam says) for shorter wavelengths because the difference in length scales is getting smaller, but it also depends on the ‘stiffness’ of the spring attaching the electrons to the nucleus — this is called the index of refraction, and it depends on the details of the atoms and molecules doing the scattering.

This doesn’t really change for solids. The atoms are still way smaller; all that is different is that they’re packed closer. They’ll have a very different index of refraction because the ways electrons are bound to the nuclei are quite different, but visible light is still basically a featureless electric field on these scales. If we think about transparent materials like diamond (crystalline = ordered) or glass (amorphous, disordered), or indeed liquid water, their index of refraction is very different than air (so you get partial reflections at the surface and changes in direction etc), but once the light is in the material it doesn’t scatter much. So the idea of disorder at these scales (Vinai’s (2)) doesn’t really matter. More important is the fact that these materials are uniform at scales of a half a micron or so. This is not the case for most solids – crystal domains, defects, polymerization patterns, biological features, large suspended particles (like in milk, paint, or clouds), thin films etc. all have structure on these length scales, and so scatter visible light strongly. Indeed even in a pure diatomic gas, when you get thermal fluctuations at the same scale as the light you get strong refraction – this happens in a rather dramatic way (look up critical opalescence) close to the critical point where there are fluctuations at a huge range of length scales.

Since X-rays have wavelengths of the order of the spacing of atoms in molecules and crystals, they scatter in complicated ways off the atomic-scale structures and you can back out information about, e.g. crystal and protein structure.

All of this has been more or less classical in terms of understanding the interactions between photons and electrons, and the accelerating charges are slight shifts in the electrons and nuclei of the atoms. But of course you can do more dramatic things to atoms for which quantum mechanics really matters. For instance, if you think about light with somewhat longer wave lengths, say about 15 microns, the absorption by carbon dioxide is so strong that the atmosphere is completely opaque. This is because the frequency of the light is just right for vibrating the co2 molecules, so the photons are much more likely to be absorbed.
I don’t think there is a truly satisfying way of answering why this is much more likely than Rayleigh scattering (to address Vinai’s rabbit hole) without appealing to the full theory of quantum electrodynamics, but there is *some* relevance to the idea of a resonance – i.e. if you push a swing at the right frequency you can get it to go way higher than if you push it at the wrong frequency. In both cases you do work on the swing, but in the first case it absorbs way more energy.

In a gas molecule, there are a relatively small number of ways to push charges around (vibrations, rotations, electron shell jumps; these latter are more likely to be present in the visible part of the spectrum, the former in infrared). These give rise to isolated spectral features where light is selectively absorbed or emitted. Not many of these happen to be in the visible spectrum for the gases which make up our atmosphere (which may be why eyes evolved to be sensitive to this part of the EM spectrum).

So what’s different about solids? In this case the nuclei of atoms tend to be within a nanometer (or less really) of each other, which means the valence shell electrons don’t just ‘orbit’ one atom, but instead are distributed across the material. The quantum states for electrons are no longer isolated, but are dense across ranges of energies called ‘bands’. In insulators like glass and diamond, these bands are either completely occupied by electrons, or completely empty, and they are separated by a large gap on the energy scale of visible photons — which makes it hard to move charge around (and therefore also to scatter visible light). In a conductor, the full bands and empty bands overlap, so it’s very easy to move charges around. If the surface is well polished over many wavelengths, you get the reflection Adam described. But there are also lots of other ways that electronic transitions are modified around defects and dopants so that you can still get rather localized spectral features that are one way to give you pigment in crystals or in coloured glass. So being uniform on scales of half a micron is necessary for transparency (to visible light), but not sufficient.

What about gamma rays and leaded glass? Well, doping glass with lead doesn’t change the uniformity on the scale of visible light, and lead doesn’t have spectral features in the visible range, so as long as there’s not enough lead to turn the glass into a conductor, it’s still transparent. Gamma rays are more energetic than x-rays which means their wavelength (10-3 nm) is much smaller than the spacing between atoms. So classically you don’t get much scattering. But because the photons have so much energy, you really can’t ignore the fact that the waves themselves are strongly quantized – and in many ways they look like particles. The main processes by which they interact with matter is through a) the photoelectric effect (at lower energies) b) compton scattering (moderate) and c) pair production (higher). All of these are very quantum.

1. All of the energy of a gamma ray is absorbed by an electron, which is plenty to kick it right out of the atom. Visible light can’t do this except for relatively weakly bound electrons. It’s most probable when there’s just enough energy to free the electron and rapidly becomes less likely – again why this is less likely boils down to QED (and I can’t help you here but I can imagine that the different length scales of the photons are relevant here).
2. In this case the gamma ray ‘ricochets’ off of an electron, sending it off at relativistic speeds and yielding another (albeit lower energy) gamma ray.
3. Here the gamma ray basically turns into an electron and a positron – so it needs to be energetic enough to produce the mass of the latter.

You’ll note that none of these directly involve the nucleus (though the latter apparently needs to happen in the large fields close to the nucleus) – you need yet more energy to interact directly with the nucleus. However, if you want to absorb gamma rays, in general you win by putting more electrons in their way. Lead has lots of electrons (and it’s probably cheaper and plays nicer with glass than other heavier atoms, not to mention less radioactive), hence leaded glass.

Radio waves are even bigger (mm to km), so atomic structure is pretty irrelevant classically, but if you have a conductor that’s big enough, that absorbs them strongly (e.g. antennae). They are also low energy photons so classical ideas work pretty well.

Ok, that was ridiculously longwinded. Have a cool gif

#### Philip Dilts

This is great! And thanks for the pictures! Once in a while I go on a physics binge on wikipedia to try to figure out the universe. Now it’s coming to me!

I did deal with EM waves when I was doing event-related potential (ERP) experiments. Basically, you put an EEG cap on someone’s scalp and detect tiny fluctuations in the electrical field caused by groups of firing neurons as their brains process them. EEG has very good temporal resolution for us but not much spatial resolution because the waves are scattered  (field is distorted? Help?) by the brain and the skull and the scalp. So, if I present you with a word or a picture, I can see something interesting happen within about 50 milliseconds, but I can’t tell you where in the brain it’s happening with any confidence. fMRIs have the opposite properties – great (mm) spatial resolution but poor temporal resolution. In MRI, a giant magnet generates and then releases a strong magnetic field in the brain and waiting for the atoms to emit radio waves. You can tell what’s where because different types of atoms emit radio waves at different rates once the field is released. Why is this the case? I, like the Insane Clown Posse, do not know. But, thanks to this thread, I understand why the radio waves are emitted without as much scattering, making it easier to tell where they’re coming from.

Functional magnetic resonance imaging works by focusing on the iron in blood. More active parts of the brain need more oxygenated (and thus iron-rich) blood, so you can see what parts of the brain are working harder by where there’s more iron. It’s hard to tell to within more than about 1-2s of precision when the brain activity changes, though, because of how long it takes to generate the field and wait for the… electrons to go back to ground state? At any rate, you get one picture for each loud knock of the MRI machine.

This was a problem for us. Like a lot of psychological experiments where you’re looking for unconscious reactions, we were looking for a physiological response that correlates to surprise. If you’re surprised by a word for some reason, at around 400msec after it hits your retina you’ll have a slightly more negative electric field somewhere in your brain. (You can even detect different levels of surprise – if I show you “the person ate the pizza”, “the person ate the beer”, and “the person ate the rock”, “pizza”, “beer” and “rock” should generate increasing strengths of negative potential.) At any rate, an fMRI that generates a picture every two seconds would obviously have no chance of detecting this difference.

#### Vinai Bhagirath

I’ve been reading and thinking about this some more, and it’s led me to question, “What do I mean when I ask, ‘Why does a phenomenon occur’?” This came up because I found that all of the “explanations” end up being “descriptions” of what is observed. This, of course, makes perfect sense, because that is what science does. I think what I mean when I ask “Why?” is: “What are the minimum requirements for this phenomenon to take place?” Or (which I think is equivalent): “What is the most general way of describing the circumstances under which this phenomenon takes place (that remains consistent with observation)?”

So, “Why is matter opaque sometimes to some electromagnetism?” is really asking “What are the bare circumstances required for matter to be opaque to electromagnetism?” This is perhaps an obvious point for some of you, but worth dwelling on. The way to get to it is to observe interactions between the individual components of matter and electromagnetism, and start putting them together in different ways, and I am sure that this is what physicists have done. I suppose it is called science.

Peter says re: Rayleigh scattering, “the directional dependence of the scattering is pretty simple.” Not simple enough for at least one of us! Can someone confirm that I’ve got this right: in glass or water, the summation of the wave goes in the same direction as the incident wave. Why doesn’t this happen in Rayleigh scattering? What is different about the interaction between the matter in Rayleigh scattering and the matter in glass? I think it is because in Rayleigh scattering the particles are not uniformly distributed on the scale of the wavelength of the light. So, you don’t have this effect of the induced lateral waves canceling out and the “forward” waves not canceling out. (From a classical perspective) Is this true? I imagine taking a transparent glass block, shattering it into uniform small glass spheres, and suspending those uniformly in space. If the suspension is perfectly uniform, would it still be transparent? Water and oil in a vinaigrette is a good example of a suspension that is not perfectly uniform. From a quantum perspective, I guess you work out the probabilities of all the possible interactions, superpose them, and find the probability of the result. How might one think of Rayleigh scattering from a quantum perspective (if possible to explain without totally leaving behind all analogy and resorting to pure descriptive maths)?

-Vinai

When Peter said that the directional dependence of Rayleigh scattering is “simple”, I suspect he meant that its functional form is simple. The derivation is at a second- or third-year undergraduate level, so in that sense, it is simple only relatively.

The radiation pattern of a dipole goes as sin^2(\theta) (the aforesaid simple function) where \theta is the angle away from the axis of the dipole. Thus, a dipole radiates most efficiently in directions perpendicular to the axis, and not at all along the axis. However, the dipoles in the molecules in the atmosphere are randomly aligned (if I am not mistaken), so the net effect is that the scattering is isotropic.

Now, there are two ways of thinking of Rayleigh scattering that I think make sense. First, you can think of the incoming light from the sun as a plane wave. In the classical analogy used earlier, the molecules are like very slender pencils interrupting a much larger wave. So the wave will largely remain a plane wave, but there will be a weak component that is scattered in different directions. Now, the pencils are not circular, but have a shape such that the wave each one produces when the water wave hits goes as sin^2(\theta). But each is oriented differently, so the individual shapes of the scattered waves get lost and the net result is that a small component of the total wave goes off in all directions as it moves through the field of little, oddly shaped pencils.

You can also think of the incoming light as a stream of photons. Each photon has a probability of exciting the molecular dipole and being re-radiated in a different direction. The probability of that direction goes, again, as \sin^2(\theta), where \theta is the (random) alignment of the dipole in the molecule. The probability that this excitation will occur, as discussed earlier, is wavelength dependent. At all wavelengths, most of photons pass through the atmosphere without scattering. (Otherwise, you wouldn’t be able to see the sun: you’d just see an atmosphere that glowed smoothly everywhere.) But blue photons scatter far more often that red photons, and hence the colour of the sky.

I’m not sure if this answers your question or not. In solids, as Peter pointed out, the electrons are generally not localised, so a lot of the time the transparency or opacity doesn’t depend on structure of the lattice of the solid but rather on what bands of energies the electrons are able to interact with, except in cases where quantum effects are important, as in the cases he gave above.

When I first read your post, I mistakenly thought (for some reason) that you were asking about why light bends when it enters glass or water, and wrote the paragraphs below. Even though they don’t answer any of your questions, they may shed some light (pun intended) on the discussion.

<Start of paragraphs on light bending.>
Now, as for water bending in light, it’s probably best not to think of this as scattering at all. The electrical properties of water are different than that of air and so there is a different index of refraction: i.e., the speed of light is different (by about 30%, which is why the bend is so easy to see). True, the photons are interacting electromagnetically with the charged particles in the water (as they were in the air, for that matter), but it’s not helpful to think of photons scattering off of individual particles.

As for why the speed of light causes it to bend, there are a few ways of looking at it that are formally equivalent. I find an appeal to conservation of momentum most intuitive. (This might also be the most naturally “quantum” explanation Vinai was looking for because you can think of each photon as having a momentum.) I was about to write an explanation here, but I found that Wikipedia explained it pretty well, so I’ll refer you there! (Perhaps you will remember Snell’s equation from our classes together at the OSCSS. I think that was covered in class!)

By the way, both of these phenomena (Rayleigh scattering and changing index of refraction) are classical, in the sense that you don’t need quantum mechanics to derive them or to understand them.

# Updating Debian to a Shellshock resistant Bash

If you have a www facing server running bash, type the following into a terminal:

$env x='() ; echo vulnerable' bash -c "echo this is a test" Are you vulnerable? You should probably fix that… If you’re on a Debian base, you can use the Bash package from Squeeze-lts$ sudo nano /etc/apt/sources.list

Add the following to the bottom of the file:

deb http://http.debian.net/debian squeeze-lts main contrib non-free deb-src http://http.debian.net/debian squeeze-lts main contrib non-free

Update apt-get:

$sudo apt-get update Install JUST bash:$ sudo apt-get install --only-upgrade bash

Remove or comment out the source list lines to Sqeeze-lts:

$sudo nano /etc/apt/sources.list #deb http://http.debian.net/debian squeeze-lts main contrib non-free #deb-src http://http.debian.net/debian squeeze-lts main contrib non-free Update apt-get again:$ sudo apt-get update

Make sure you’re patched

$env x='() ; echo vulnerable' bash -c "echo this is a test" Best of luck. # Why I tend to support the donation fads/memes that sweep social media. The ice bucket challenge has thoroughly infected Facebook. What a great example of the cliché ‘going viral’, with nearly everyone who participates faithfully following instructions to ‘infect’ three more people once they’ve accepted their drenching. It’s super funny, because, you know, ice water on your friends. The peer pressure is approaching Mariana Trench levels, and tons of A-list, B-list, C-list, and D-list celebrities have jumped on-board, so we’re all practically rubbing elbows with Bieber and Cat Deeley. It’s fun, doesn’t take much effort or time, and we’ve been told it’s for a good cause. Social media success story! LOL #awesome #IceBucketCatVideo And the backlash. It’s just slactivisim! All you water wasting sheeple are a bunch of narcissists, patting yourselves on the back for doing something trivial to ‘support’ a charity you know nothing about. You aren’t actually DOING anything to fight ALS! It’s not like you’re spending time to find a cure, or caring for the sick, or supporting the families and loved ones of those affected. Hell, 99.9% of people doing the ice bucket challenge have never donated a penny to ALS before, and if the marketing team at www.alsa.org had of been working for the spina bifida foundation, or the elephantiasis care center, you’d still all be dumping water on yourselves like morons. Come on people, hardly anyone even has ALS! Donate to cure something like heart disease, or diabetes, or cancer. #GroupThink #PeopleAreStupid My opinion? Well, yes, these fads do tend to be a touch narcissistic (my Movember mo was really, really, awesome) and self congratulatory (all three times). It’s true that the vast majority of people who propagate the memes have never been, and will never be, personally involved with the organization(s) they are arbitrarily supporting. And I will even concede that there may be a lot of people who completely miss the point that all this fun on Facebook is actually a fund raiser. But none of that matters. ALS afflicts less than 0.01% of the population, meaning hardly anyone cares about it, and it isn’t a big ticket item when funding cycles roll around. Now, because of a fun internet craze, the ALS Association and its international partners just received a massive windfall of public awareness. Not to mention$100 million of unexpected money, with little-to-no overhead attached to its collection. So that’s a demonstrably positive outcome for a charity that seems to have done a decent job with donations in the past (charity navigator). To be honest though, I think the benefits to the ALS association are beside the point. Even if half of the people partaking in the challenge have no idea what it’s for (and I think that’s unrealistically pessimistic), millions of folks will still have gone on-line to do a little research. They check out what ALS is, and let’s say 50% of those people drop off there. The rest, however, will probably keep poking around a bit more. What’s a neurodegenerative disease. What are some other neurodegenerative diseases? How are they treated, and how might therapeutic stem cells be of use? What could I do to help? It really doesn’t matter if it’s the ALSA, or the spinabifida foundation, or the elephantiasis care center (which don’t actually exist, btw), as long as it gets a sizable chunk of people thinking about health/medicine, science, and philanthropy. I’m also not in the least bummed out that all those donations to the ALSA may have a (probably small) impact on donations to other medical charities this year. It’s not like the scientists who get the grant money are going to keep all their findings in a secrete Lou Gehrig’s vault. Any advances in understanding or treating ALS will probably be equally important advances in general neuroscience. Most people are obviously not hating on the Ice Bucket Challenge (or Movember, or the Ride for Heart, etc), but I’ve seen enough cynical comments/articles that I thought I’d add my two cents.

And come on! It’s super funny, because, you know, ice water on your friends.

# Because sometimes a blog is simply the right forum

I tried blogging a few years ago, one post per day, for a solid 30 days. It was fun but the daily post was a little stressful, because I’m a horrendously slow writer. That blog no longer exists.

Here’s another blog, and it’s not going to be a daily update. I just want a little chunk of the www where I can put things that are a little more long winded than are really appropriate for Facebook or Twitter. I might even make it look nice one day.