Ask HN: On Systems Engineering (EE) vs. Systems Engineering (CS)

I'm entering my Senior year of college with dual majors in Systems Engineering and Physics. I've also started a couple companies and love both coding and the startup lifestyle. (Details on my profile page, if you want more details/contact). My flavor of Systems Engineering resembles Electrical Engineering with an emphasis on control theory and operations research. With the latter concentration specifically, the algorithms/heuristics behind seemingly basic apps like the Google Maps algorithm have fascinated me. In fact, it is these OR professors who describe a tangible engineering problem, the go to the board and write the problem in flawless mathematical set notation, then finally show us the code that applies OR techniques to find a solution that I find truly inspiring as I begin to make post-graduation plans (for it spans engineering, pure mathematics, algorithms (physic-style!), and computer science). On a more personal level, it surprises me that such few students take operations research classes, when it seems that the techniques taught are in use on a large scale in both consulting firms and corporations to save billions of dollars a year in inefficiency. However, when I look at startups and find positions for 'systems engineering,' they tend to involve low-level C/C++ programming, the Linux kernel, and DNS. I understand their use of the phrase as it applies to the engineering of a computer system. However, this strongly differs from the academic definition, both in skill set and application. The dichotomy here confuses me. I enjoy perusing the job postings of my favorite startups, and finding that the title on my degree in no way applies to the same title on a job post is a bit disheartening. The skillset for the computer science 'systems engineer' does not seem to intersect with even the basic accreditation requirements for a person to considered a legally-qualified professional engineer, let alone the academic definition of a systems engineer. Can anybody comment on this? I feel that I am looking for insight on: * how the industry should approach computer system experts * how systems engineers from the academic/EE perspective should market themselves in the hacker world * whether this fuss is a bit inane because my major is considered both interdisciplinary and amporphous Also, on a more personal/curious level: Can anybody recommend a few books that teach the skills of a CS systems engineer? I understand the basics of the Turing theory, have extensive electricity and magnetism background, and know Python/Java/Ruby/PHP/Matlab/RelationalDatabasing/NoSQL, but: I don't understand the Linux kernel, low-level systems processes, or the more low-level DNS functionality. I have a voracity for understanding technology and really wish to add comprehension, if not a higher level of educatation, of the CS systems engineering to my repertoire. (i.e. I'm an EE systems engineer, but this CS systems engineering stuff seems cool and I want help learning it!)