Emil, if the size of the photosite is correlated to the size of the pixel and the size of the pixel is correlated with pixel level noise, then by logical inference the size of the photosite is correlated with the level of noise, ceteris paribus, is it not? The reason why I mentioned firmware is that the camera's firmware - AFAIK - does the analog to digital conversion and the manner in which that happens should have some impact on the qualities of DR and apparent noise when we open the image in Camera Raw - would it not? (i.e. please clarify what I may ne misunderstanding here.)
I don't understand your last para - "do about the same" is in regard to what? The D3 is coming out slightly ahead in respect of what? Does the last part of the statement mean that the differences in noise are far less than the differences in pixel pitch between these cameras?
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The size of the photosite is correlated with the *pixel* level noise, what you see when you view the image at 100% on a monitor. Noise has a scale dependence. Suppose we combine the output of a 2x2 block of photosites. The signal is additive -- one just adds the photon counts from all four. Noise adds as RMS -- the sqrt of the sum of the squares of the pixel noises. This means if all are about the same, signal goes up by four, but the noise only goes up by two, and so the S/N ratio improves if we halve the resolution.
It is easy to see this for yourself. Open a new canvas in photoshop, fill it with middle gray and add a bunch of gaussian noise (Filter>Noise>Add Noise). Now go to the Gaussian blur filter and watch what happens to the width of the histogram as you change the radius of the blur. Increasing the blur radius decreases the image resolution; it also decreases the noise.
So if you properly resample say a 1Ds3 image to the resolution of a D3, the apparent one stop pixel level noise advantage of the D3 drops to something on the order of 20%. That 20% can be understood from the fact that the D3 is 20% more efficient per unit area at collecting photons than the 1Ds3. So the 1Ds3 has higher *pixel* level noise, but *image* level noise -- noise measured at the same spatial scale -- is not all that different. Now, that near equivalence is there whether we resample/blur the 1Ds3 image or not, since the same photons were collected by the sensor whether we bin the pixel samples together or not. Since noise goes as sqrt of signal, that 20% difference in photons is only about a 10% difference in noise amplitude to the 1Ds3's detriment; on the other side of the balance sheet is a 32% increase in linear resolution.
It is thus important when comparing noise figures to compare them at the same scale; any pixel level noise measurement should be divided by the square root of the MP count to normalize relative to a consistent and comparable percentage of the frame size. If one wants to extrapolate -- eg imagine how a full frame sensor tiled with 40D pixels would perform -- one should multiply the pixel level noise of the cameras to be compared by the respective pixel pitches. By this measure, the 40D, 1Ds3, and 1D3 have about the same noise at comparable scales, even though their pixel level noises are quite different (and larger the smaller the photosite is). One way to understand this is that Canon did their job right, and all three sensors are capturing the same number of photons per unit area. BTW, some people have speculated that the reason the D3 does about 20% better is that its microlenses purportedly have about 20% better area coverage.
As for analog-to-digital conversion, that is done in hardware, not firmware; the only way that firmware could have an effect is if the camera is doing some processing of the sensor data before it is written to raw (eg noise reduction), and I have seen no evidence of that under ordinary shooting conditions (not at all in Canons with default settings; Nikon does some NR on raw for exposures of 1/4 sec and longer but not otherwise).
The reason MFDB's do so well is that they have twice the sensor area of 35mm, so gather more photons; the size of individual pixels matters little in this regard.
Sorry for the lengthy diatribe...