Because the jpg has been processed.
The camera has full access to all the data from the sensor.
The jpg has been processed by the camera according to what it thinks is best.
The jpg only has a small amount of this data and been processed automatically.
The .NEF is the full raw image data. It has much more data which gives it much more latitude when editing.
Think small garden hose vs fire department hose. In image editing, more is better!
Since you are using a D3 you obviously care about image quality.'
You should be editing the .NEF.
Jpgs are ok for snapshots when you just want an quick image, not concerned with image quality and have no plans to edit it.
The in-camera generated JPEG has been processed with Nikon's built-in software following what Nikon thinks the image should look like. You would get the same result if you use Nikons's stand-alone raw-editing software on the raw NEF at its default/or auto settings.
In contrast with that, Adobe Camera Raw is not meant to emulate Nikon's software or what the camera thinks it's best, but designed to result in what Adobe considers the best rendering possible of the raw file or whatever you think it's best. You do have to learn to use Adobe Camera Raw proficiently, of course.
Once you thoroughly master the use of ACR, you can emulate any other rendering, including the results from the camera if that's what you want—except that in that latter case it makes little sense to shoot raw.
I do not understand the second paragraph - do you mean that Adobe Camera Raw provides access to all of the raw data from the camera? If that is the case then why would the jpg file opened with Adobe Camera Raw differ from the same nef file opened directly in Photoshop? (Most notably in the histograms.)
The primary goal is to edit raw data and not necessarily Nikon's or Adobe's processed data. I have been shooting raw for ten years under the assumption that raw was virtually equivalent to film negatives; and I saved negatives. I was hoping (naively) that perhaps in the digital age Adobe Camera Raw would allow me to just save the "prints".
Please reread the explanations. Nef and RAW are both the camera data without processing and are not altered by the processing. They remain as shot. Editing creates aversion which you will save. jpgs from the canera have been processed
according to Nikon's idea of imaging. If you edit in ACR and save as jpg and open in PS then you hace YOUR idea of what a jpg should be.
The primary goal is to edit raw data and not necessarily Nikon's or Adobe's processed data. I have been shooting raw for ten years under the assumption that raw was virtually equivalent to film negatives; and I saved negatives.
That assumption is correct. A RAW file is considered to be a digital "negative".
I was hoping (naively) that perhaps in the digital age Adobe Camera Raw would allow me to just save the "prints".
ACR allows you to create a practically unlimited variety of "prints" from a "negative" with far greater ease than you ever could have done with film.
I do not understand the second paragraph - do you mean that Adobe Camera Raw provides access to all of the raw data from the camera?
Of course it does.
Despite your having "been shooting raw for ten years", you need to do a lot of reading on the subject to comprehend what a raw file is.
A raw file is a linear, undemosaic'ed image file that contains nothing that a human being can discern as color, just a very, very dark grayscale picture as seen by the camera sensor.
In order to see it, the raw data has to be rendered, demosaic'ed or converted (all functional synonyms) by specialized software. That software can be either the software (firmware) built into the camera by the manufacturer or an external, standalone application provided by the camera manufacturer or a third party like Adobe, which is the case of ACR (Adobe Camera Raw).
Now, it so happens that Nikon and Adobe have different criteria and ideas as to what the original image looks like or should look like.
If you look at both the raw and the JPEG in Nikon's software at its default or auto settings, they will presumably look pretty similar. Not exactly the same, mind you, because the JPEG has the baggage of compression artifacts even at maximum quality settings and a narrower color space (either Adobe RGB or the infamous sRGB) than the wider gamut provided by the converter.
When you view them in Adobe software, the differences will be substantially more pronounced between the two images, because the JPEG was generated from the raw data in-camera by Nikon software while the rendering of the raw is provided by Adobe software (Adobe Camera Raw, ACR) which does not follow Nikon's rendering because it is specifically designed not to in order to give you the best possible starting point for editing your image.
…If that is the case then why would the jpg file opened with Adobe Camera Raw differ from the same nef file opened directly in Photoshop? …
I just explained that to you in this post (and I thought I had before as well ):
The JPEG contains no raw data whatsoever, it has already been "cooked" in the camera, ergo it's not raw anymore. (As an unabashed JPEG hater, I do not hesitate to express it in terms of the JPEG already having been messed up or worse (f***'ed up) in the camera.)
Photoshop cannot directly open any raw file, NEF or otherwise, it has to call on Adobe Camera Raw to do it. Photoshop cannot read raw data at all.
Do a Google or Amazon.com search on camera raw Jeff Schewe and/or digital negative Jeff Schewe for some essential reading you should do ASAP.
Bottom line: one has to learn how to use Adobe Camera Raw proficiently.
Ten years? And you don't know what it is? That sets some kind of record.