The chromophore of rhodopsin is actually retinal (not retinene). The molecule has an aldehyde group at the end, which makes it easier for the protein to “grab hold” of it. The absorption of a single photon (by the conjugated double bonds mentioned by Blake) induces an isomerisation reaction, from 11-cis retinal to all-trans retinal (single C-C bonds are free to rotate but double C=C bonds have a constrained shape, but there are two possible ways that a long molecule can incorporate C=C double bonds ; the terms “cis” and “trans” [more correctly termed Z and E, but biochemists use many outdated chemical terms] indicate the two options). This isomerisation changes the shape of the chromophore, which causes a conformational change in the rhodopsin (so the protein also changes shape).

From here on in, I’m a bit hazy on the details, so some of this might be a little bit wrong. What I think happens is the opsin, in its light-activated form, becomes a substrate for a kinase enzyme that adds a phosphate group to a specific site in the opsin molecule. This phospho-opsin itself has a kinase activity that phosphorylates another protein, activating that protein’s kinase activity. Two or three generations of this activity lead to a massive amplification of the “signal” and end with the release of neurotransmitter molecules across the gap from the rod cell in the retina to one nerve cell in the optic nerve. Thence, the signal is propagated in the same way as any other nerve impulse. Once it reaches the visual cortex, I have no idea how that impulse is turned into a part of an image.

Hope this sheds some light on your question.

Get it? Sheds light … oh, never mind.

I’m also surprised that no one seems to have brought up Larry Niven’s The Integral Trees yet.

PS: The first “It’s” should be “Its”.

Thanks Thanks … I don’t remember much of my fundamentals anymore but I don’t think anyone ever said that “So, if you want the bumper-sticker version, the electromagnetic field is made of photons.” So photons are not creations of E&M oscillations but instead the fields are the way we describe a collection of photons…

but but but

“Photons are quintessentially quantum beings, and we are simply too **big** to experience things behaving in a quantum way.”

they must tbe something. I mean if you look at an electron as a, what, de Broglie wave, or something, its described with probabilities and such.

its a thing. so what is a photon, a little packet of energy? is it discrete? point? a squashed probabilty function?

I know a photon is both a wave and a not-wave but I just wonder how to describe it roughly as a “point charge” is, in a non-quantum way.

Anyway thanks for the info, you obviously know what you’re talking about.

kd

Kevin:

Photons do not “carry” an electromagnetic field along with them as they travel. Instead, they **are** the field: when we talk about a single atom, it is often most convenient to describe the atom picking up and giving off energy in “lumps”. We can idealize the situation somewhat and say that the atom emits or absorbs particles, the energy of each particle depending upon some number associated with it. The difficulty is that these photons, like everything else on the atomic and sub-atomic scales, do not behave like anything we have everyday experience with. They do not act like billiard balls; they do not act like grains of sand. Photons are quintessentially quantum beings, and we are simply too **big** to experience things behaving in a quantum way.

If we have a whole bunch of atoms, all emitting or absorbing light together, then we can treat the vast collection of photons involved as a simpler entity. Instead of trying to imagine all those fast-moving, counterintuitive photons, we approximate the true situation, and we say that there is a “field” extending throughout space and time. Mathematically, this “electromagnetic field” is a set of numbers associated with each point in space; because our brains are good with pictures, we often draw the field as a bunch of lines with arrows on them. Lines come out of some charges (the kind we call “positive”, an arbitrary choice going back to Ben Franklin) and coverge towards others (the ones we call “negative”). Wiggle the charges and you get wiggling lines, oscillations whose behavior you can predict using the Maxwell equations.

Steven Weinberg called the electromagnetic field “the tension in the membrane, but without the membrane.”

On the quantum level, “electric charge” is a property of the fundamental particles — electrons, quarks and so forth. A particle is “charged” when it can emit and absorb photons. When a charged particle absorbs or shoots out a photon, we call the event a “coupling”, and the strength of the electromagnetic force depends upon the “coupling constant”, which gives the probability that a coupling will occur. (I’m skipping all sorts of lovely details about virtual particles, polarizations and so forth.) To put it imprecisely but vividly, when you shake a charged particle, photons come flying out. You are correct in saying, “photons get killed all the time”. It’s not a tragedy — that’s what makes ordinary matter possible!

Because the Maxwell equations predict that disturbances in the field travel as waves, physicists got used to discussing light in terms of its “frequency” (the number of oscillations per second) or its “wavelength” (the distance between successive wave crests, the frequency times the speed of light). We can say that each photon has a “wavelength”, which is the number I mentioned earlier that determines the photon’s energy. It is a little weird to discuss the “wavelength” of a single particle, but quantum particles are intrinsically weird, and that is just the way Nature works; this is the domain of the famous two-slit experiment.

So, if you want the bumper-sticker version, the electromagnetic field is made of photons.

It is interesting to ask, “What would happen if the photon itself had an electric charge?” See, charged particles like electrons and positrons can “couple” with photons, but photons do not couple to one another. The theory would get horribly more complicated if they could, and the “classical theory” (the approximate theory we use to describe large objects) would no longer look like the Maxwell equations. Nature has in fact given us an example of this kind of theory: in the strong nuclear interactions, the analogue of charge is a property called “color” — nothing to do with ordinary color, just a name physicists use because we ran out of nice Greek words. Particles which have this “color”, like the quarks which make up protons and neutrons, emit and absorb “gluons” just as electrons couple with photons, but gluons **also** have color: they can couple directly with other gluons, causing all sorts of wonderful complications.

The best book I know about on photons and such is Richard Feynman’s **QED: The Strange Theory of Light and Matter**. James Gleick’s biography of Feynman, **Genius**, does a pretty good job of explaining the relation between quantum and classical theories (there’s at least one other biography of Feynman, but I haven’t read it). Larry Gonick and Art Huffman’s **Cartoon Guide to Physics** is also worth sinking one’s teeth into.

And now that I’ve mentioned Feynman, I might as well say that chapters 35 and 36 of his **Lectures on Physics**, volume 1, go into loving detail on how color vision works. I quote from section 36–3, “The rod cells”, which describes the molecule of retinene:

“It has a series of alternate double bonds along the side chain, which is characteristic of nearly all strongly absorbing organic substances, like chlorophyll, blood, and so on. This substance is impossible for human beings to manufacture in their own cells—we have to eat it. So we eat it in the form of a special substance, which is exactly the same as retinene except that there is a hydrogen tied on the right end; it is called vitamin A, and if we do not eat enough of it, we do not get a supply of retinene, and the eye becomes what we call night blind, because there is not then enough pigment in the rhodopsin [the purple pigment in rod cells] to see with the rods at night.

“The reason why such a series of double bonds absorbs light very strongly is also known. We may just give a hint: The alternating series of double bonds is called a conjugated double bond; a double bond means that there is an extra electron there, and this extra electron is easily shifted to the right or left. When light strikes this molecule, the electron of each double bond is shifted over by one step. All the electrons in the whole chain shift, like a string of dominoes falling over, and though each one moves only a little distance (we would expect that, in a single atom, we could move the electron only a little distance) th enet effect is the same as though the one at the end was moved over to the other end! It is the same as though one electron went the whole distance back and forth, and so, in this manner, we get a much stronger absorption under the influence of the electric field, than if we could only move the electron a distance which is associated with one atom. So, since it easy to move the electrons back and forth, retinene absorbs light very strongly; that is the machinery of the physical-chemical end of it.”

What we really need is a They Might Be Giants song explaining all of this.

Blake

It’s extremely complicated! An excellent website to learn about all this stuff is analemma.com.

Not totally sure I’ve got that the right way round, or even when apoapsis and periapsis are.

Here’s a question for the astronomers out there. This is driving me crazy. I know there must be a simple explanation, but I can’t work it out. Help me. Here goes: As we approach the winter solstice, I take note of the lengthening darkness and shorter daylight hours. There is an anomaly (?) however, that baffles me. Over the last four to six weeks, sunrise in my area comes about a minute later each day, but sunset advances at a much slower pace. For example, in the last few weeks, sunrise has gone from 7:20 to 7:40 am, while sunset has only moved a few minutes – from about 5:08 to 5:03 pm. How can this be? It must have something to do with latitude, right? Mine is 39 degrees, 20 minutes north. Someone explain it. My intuition tells me that sunrise and sunset should advance (and recede) nearly equally. But that is not the case. Why? Thanks.

“light travels as waves IN electric and magnetic fields and is a lateral wave”

but don’t photons just travel through space where there are no electric and magnetic fields? I thought they somehow “carried” the energy of a photon AS an E&M field, continually oscilating between them. I mean I studied Maxwells equations and I can’t say I understand them but when I talk about a quanta I have a hard time thinking of it as a construct of an interaction will an external field.

“It may actually knock an electron out of its orbital altogether, in the which case its energy is converted to electrostatic potential energy ” which I sort of got to on the ride home because even if “It may remain as an excited electron for a while and re-emitted at the same energy” for the time it was bound to the electron. its NO LONGER a photon because its lost its E&M waves…. (is that right?) as exists only as “electrostatic potential energy ” (electron in a higher orbit) so I think that photons get killed all the time and we always get new ones when they are emited .

So now next question, when a photon hits our photo-receptors, what happens? and how cool is it that E&M radiation of all types has so much information in it?

Can temperature gradients exist to produce visible circular rainbows?

I worked on proto-stellar disks of pre-main sequence stars for a while, reducing the images and spectra taken by STIS on Hubble. That was awesome work, probably my favorite of all the things I did with Hubble. The images were beautiful, and challenging to work with (I wrote my best piece of software ever to subtract a star profile from the image to leave just the dust disk image). I’ll write more about that someday, though I did write a bit about it here.

Kevin, there is a fundamental difference between light ands sound waves : light travels as waves in electric and magnetic fields and is a lateral wave (oscillations perpendicular to direction of travel) whereas sound is a mechanical vibration of molecules and is a longitudinal wave (waves of compression and expansion that oscillate in the direction of travel). OK, light is also a particle, but in some situations it helps to think of it as a wave.

When a photon of light is absorbed, it can have several diferent fates, largely depending on how constrained the orbital of the electron that absorbed it is. It may remain as an excited electron for a while and re-emitted at the same energy. It may be re-emitted in steps as lower-energy photons (which is how fluorescence works – a UV photon absorbed and then re-emitted as visible light). It may actually knock an electron out of its orbital altogether, in the which case its energy is converted to electrostatic potential energy that can become some other form when the free electron is subsequently re-bound by another atom (in principle, this could be a photon of the same energy as the original, but it could be several other things too).

>Does that mean there are planets in the ring, or on either side of it?

If I understand what the BA was saying about Saturn, it is planets on either side of it that sweep up the matter in those regions, clearing them out. They also to some extent will shift some dust orbits inward or outward. The inner ones pushing inward send it to the star, pushing outward intothe belt. The outer ones pushing outward to away from the system, inward to the belt. Ergo, a shepherded ring.

The proto-planetary is the sexiest of the 3 of them, I can tell you. The thing is that it is extremely difficult to know for sure if we just have a star+disk, a star+disk+planets, or star+asteroids and other possible combinations. The different contributions from these different components are difficult to disentangle when we look at the object as a whole and we just measure/detect its light coming from light-years away. Just identifying a disk from the spectrum of the object is a hard job. But like BA mentioned, we have clues that help us to build the picture and refine our models.

Hmmm… monkey brains….wasn’t that in a movie?

Wonderfull thing the eye. and an odd thing that is light. what is light? EM-waves that show up as spectra? Packets that bounce into our eyes? Do we see light the same way that we hear sound?

Is light generated when electrons are accelerated? as a by product of nuclear fussion?

Does light ever get tired? I mean sound (and there hae been some great experiments using sound as a substitute for [plasma?]) gets tired. It gets absorbed. Isn’t sound just energy moving through a medium? so when the energy is dissipated the sound is gone.

So my question is when light impacts on a surface that can absorb it…e.g. er .. a black cloth? a cold black cloth? and not-re-emit it….(is there such a thing?) I assume that the quanta of energy is used to boost the level of one electron in one molecule…and it sits there waiting for some other event to release it…..

SO SO all the light created is never destroyed? That dosn’t seem to make sense.

(Or do some nuclear proccesses absorb photons? I forget.)
(Or once the electro-magnetic energy packet is absorbed and used to bind a sugar as in trees…but no cause when we burn would the energy is released. )

So is the issue that sound is an organised process, of energy organized in a wave and light is composed of discrete individually un-organized packets? of course you can organize the packets but each one is itself light, while sound cannot exist as a discrete item?

just some monkey brain ideas.

Th

James: A better place to ask about string theory would be http://www.cosmicvariance.com/ — one of the bloggers there is a string theorist, and I’m pretty sure some of the others have had experience with it. Speaking for the Zeitgeist, the title that’s on everyone’s lips is The Fabric of the Cosmos by Brian Greene. Personally, I don’t think it’s a very good book, but it may be the best pop description of string theory you’ll find.

In a side note, a request: Can you (or your readers) recommend a book about string theory for someone who is not a scientist that will explain the current state of the thinking on it. I’m very curious and a bit lost. Thanks.

Will this help us refine our models of solar system formation? At least for the sort of modeling I do (which, admittedly, is more biological in nature) more detailed information of the timing of specific stages of the process can be very helpful in certain circumstances. Assuming this is a pro-asteroid belt, having this specific information about when the asteroid belt is at this stage of development could be very helpful. Or it could be completely redundant, if it matches the models’ predictions.