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The only relevant section in the syllabus says, "Good manners provide the foundation for proper classroom behavior: arrive on time, listen attentively and take detailed notes, remain quietly in your seat until dismissed by the instructor." There is a strict no-screen policy, but nothing about reading.

I am pretty sure that all department chairs would agree with a faculty member who concluded that reading in class is the opposite of listen attentively and take detailed notes. I would put your chances at exactly zero that the chair would override the decision to not credit you with attendance on that day, but marking you as absent for two days does not seem justified unless there is another penalty for not following proper classroom behavior.

I will address two related but separate questions here: first, do you have a valid argument that the professor’s actions are unfair; and second, what should you do.

Let’s start with the purely logical issue of whether your complaint has merit. I think it does: your professor is being unreasonable and illogical and is abusing her authority. Here are several arguments that come to mind to substantiate these claims:

1. 
   

   Illogical justification for the course policy. The professor justifies her requirement that students “listen attentively and take detailed notes” with a reference to “good manners” and “proper classroom behavior”. This is illogical. In a “ginormous class” as you describe it, there is nothing even remotely improper or contrary to good manners if a student does not take detailed notes or even does not pay any attention to the lecture, as long as they are not being disruptive. The professor is misusing the English language here: just sitting quietly in a class of, say, 100-200 students and thinking about whatever one wants to privately think about, or reading educational material on an unrelated topic as you were doing, is no one’s definition of impropriety that I have ever encountered; if it were, we’d be in serious trouble by the way, since if you walk into any large classroom anywhere in (for example) the US, at any given moment you’d see probably at least half the students doing exactly that (not to mention things that may actually be considered somewhat improper, like using their phones).

   
   
   

   If the professor had just set out a policy mandating the taking of notes and attentive listening without giving a reason, one might have a harder time arguing against it (see below). But by illogically tying this to “good manners” and “proper behavior” she has undermined herself and set those rules up to be rightly criticized as being unrelated to the stated purpose they are claiming to be designed to achieve.

   
   



2. Illogical punishment. Another way in which the professor is being illogical is with the punishment she is giving you: she marked you as absent from one or maybe two lectures, but the unquestionable fact is, you were in attendance that day. Again, it is an abuse of authority and a misuse of the English language for the professor to pretend you weren’t in attendance in class when you were. Even if one accepts that she has authority to mete out some punishment for what you did (I don’t), she is again undermining herself by giving out what is an obviously unacceptable form of punishment.



3. 
   

   An abusive policy. Even if one ignores the illogical justification given for the listening rules the professor set out in the syllabus, she simply has no authority to make such requirements.

   
   
   

   Let me explain: it is usually assumed as a default premise that professors have the authority to make rules governing behavior in their classes. I see people making that assumption in some of the other answers and comments. Well, within reason, of course that’s correct, but it’s also obviously the case that no professor can mandate arbitrary rules that serve no purpose or that one cannot realistically expect students to follow, for example requiring that students wear silly party hats or risk suffering a grade penalty if they don’t.

   
   
   

   In this case, the professor is trying to force her students to “listen attentively and take detailed notes.” Unfortunately this is simply an impossible requirement to satisfy. There are perhaps 1% of students (at really good universities) who have such remarkable powers of concentration that they would be able to sit through a 50 minute lecture and not once fail to listen attentively or fall behind with their detailed note-taking. (I’m positive I don’t fall in this group, by the way, but somehow managed to be a top student nonetheless and go on to a good career as a professor. Hmm...) And if the lecture is a boring one, that percentage would certainly shrink to 0%. Humans’ brains simply aren’t wired in a way that makes it possible to comply with the professor’s requirement.

   
   
   

   Well, a requirement that the vast majority of students are physiologically unable to follow is null and void. No professor has the authority to make such requirements or to enforce them, even if the enforcement is selective and limited only to specific types of violation of the abusive requirement.

   
   

Now, I said I will discuss what you should do about the unjust treatment you are suffering. The truth is I don’t know. Appealing the punishment would make sense if you are in an environment where people care about fairness and logic, and if you did not fear retribution from the professor, but not all environments are of this type. Also, the appeal would have a real cost in time and mental energy that you will have to spend to get the outcome you believe is just; even then, success is not guaranteed.

If you do decide to appeal, try to ground all your arguments in logic as I have tried to do above. Just saying “this is a stupid policy” is not a good argument. One has to think carefully about, and make an effort to explain even more carefully, why it is a stupid policy; why allowing professors to make and uphold arbitrary rules will lead to all sorts of undesirable consequences and will result in students’ grades being less meaningful indicators of their abilities; why professors should be held to a high standard of logic and consistency in their treatment of students; and why your own behavior, even if technically in violation of some paragraph of text in some official-looking PDF document somewhere, was actually not only reasonable but actually rational, useful behavior that educators would actually want to encourage students to engage in to promote effective learning. All of those things are fairly subtle points, so the better a job you make of understanding them and explaining them to the powers that be, the higher your chances of success would be.

Good luck!

I would still take it up the ladder since that sounds like a stupid policy.

In my opinion, if she's not able to keep your interest, she should consider raising the level of the class, but there's only so much she can raise it without losing other students. It's not always possible to keep everyone's interest and you can't expect students to feign interest because it makes you feel important.

What does she care if you're quietly reading? It sounds like she childishly wants to be listened to. That's beyond wanting "good manners". She wants devotion.

You might as well complain to her dean. Even if you don't get what you want, if enough people complain, it's at least annoying for the dean who might pass the message on to her in one way or another.

Regarding some of the comments, when I wrote this answer, the only other answer here was essentially "suck it up, you have no power". When I saw that, I wanted to highlight why I think the situation is wrongheaded and unjust.

I think it's natural for professors to want the rapt attention of their classroom. But when that doesn't happen, my professors were much more mature than this lady. They did the best they could to transmit their passion for the material. In my opinion, that's the main function of education.

What happens when you try to force someone to care about something? They care less. It destroys the student's passion. If children are forced to eat something they typically end up hating it. Who fell in love with literature if not by reading great books? Who fell in love with mathematics if not by seeing the beauty of it revealed? No one falls in love by force.

If people don't care about your lectures, it's their loss. If, as a professor, you think that's bad manners, it's up to you to suck it up and just do your job as best you can. Sometimes the students are in the wrong program, and they'll find their way. Sometimes the professor is teaching the wrong class. I can't see any reason to punish someone for not overtly paying attention.

If you want to know how to diplomatically change the policy, take a look at Dan Romik's excellent answer. I don't think we should get into the habit of accepting injustices. A simple paragraph email to the dean to explain your situation might not be effective, but I think it's a good habit to get into to express yourself rather pushing down your feelings of injustice. Some words that touched me were by Martin Luther King Jr. who argued against a person:

devoted to 'order' [rather] than to justice; who prefers a negative
peace which is the absence of tension to a positive peace which is the
presence of justice.

My dean once told me, "Remember where you're sitting." Approach this with respect for the professor and from a position of strength, not with disdain for the professor and from a position of weakness. Your best chance is to ask for probation, but you must also admit a no-brainer. It's all in here, try this:

I am writing concerning the two absences I was deducted on account of reading unrelated textbooks during class. I request probation to have the statutory absences removed, but only on the condition that during finals I present responsible class notes for the remainder of the semester. As an engineering student, I should know that reading a textbook applies to the same principle as a the policy ban on mobile screens in class. Though this is an introductory class, covering information with which I consider myself to be familiar, I will hold a newfound respect for the importance of both foundational skills and the value of reviewing them. My grades are of concern to me, so if you as the lecturing professor will not grant me an achievable probation, I would only exercise my right to appeal by forwarding this same letter to the department chair, but I would go no further.

IME, this is your best chance. You can take suggestions from anyone, but it's still your own decision which course of action to take; whatever the results, the blame or the credit all goes to you.

Brief explanation: The goal is not to prove a prof wrong at the price of -5%; the goal is to reverse two special absences, and keeping peace is the best chance here. Every step of this letter does that.

To respect the community, I'm adding notes to explain, feel free to skip:

In my background, this isn't just theory, I wrote a letter to my school and had the student rules changed mid-semester. I also wrote a letter to Chicago and had the no-parking curbs painted yellow the following month. I've done more elsewhere and I know how to draft a letter that wins. The secret is that everyone needs to win and folly needs to be set in a third seat no one is forced to sit in.

No matter the outcome, no one loses face with this. If the prof permits the "probation", then the prof doesn't have to admit any wrongdoing. Never ask your opponent to admit guilt as a requirement of granting your request.

The word "statutory" is vital because in a busy administration, these must be regarded as a kind of "technical foul", not actual, normal absences. The student has three actual absences, so there is a good chance for confusion. Any other word would require more words or be confusing. This makes everything clear.

Offering to keep good notes reflects the "original intent" of the prof's policy and a "coming into the fold" to support what "good attendance" is all about. It is also a way of "eating crow", a necessity to get probation anywhere, and the student gladly wears the dunce cap, but with a straight back, self-dignity, and gratitude to the prof for a punishment well-deserved. It shows dignity across the board, including the self-dignity of growing up and becoming a better person, which is what college is all about.

Engineering students should know the cross-media application. In the 1990s and before it was reading magazines. Today, it's playing on handhelds. Engineers produce "products" that fulfill the same, age-old purposes in society, but using technology for the time and purpose. An engineer who doesn't see the carry-over will have difficulty working with a product manager in the field. Moreover, that might have been covered in one of these boring, elementary (but vital) lectures.

Foundation, foundation, foundation—that is essential to any discipline. Also, this student might need to explain these principles to a product manager or a design team one day. Listening to this prof put things in simple terms might not only be for the students to learn, but also serve an example for what the students can say to teach other departments in a future company. Showing gratitude for this teaching method's "value" is wise.

"My grades are of concern" is the toned-down way of saying "It's my prerogative", which would be too wordy. Any student should be concerned about grades; some aren't! This student is one of the good students. And, it is perfectly understandable and reasonable that a student take steps to attain better grades, even with some normal college-age immaturity elsewhere. Any decent student would be foolish not to appeal for better grades if there were grounds for an appeal. Say so!

The final sentence might wrongly seem like a threat to some people. However, this is no more than a respectful reminder of the student's own rights. Always state your rights and that you may exercise them in any administration, whether school, government, courts, or any other. If anyone might feel put off by this, that could indicate a need to either learn about respecting the rights of others or to examine one's own motives. Why would you having rights make someone else feel threatened? What kind of a person would feel threatened by someone else having rights? With such a person, there is no way to win, and there would be nothing good or kind enough to say. But, I don't think that's the case here. This prof seems like a good person who genuinely wants students to learn because, though arguably harsh, the rules aren't totally unreasonable. Such a good person as this professor should not be offended merely by someone else reminding everyone of known rights.

Stating specifically how the student would make an appeal means that the student won't try to walk on the prof, but won't be walked on either. The prof knows what would happen, no surprises. So, the prof could go to the chair first and ask first, making a decision that won't be overturned by any appeal either way. Again, this allows saving face. If the student appealed, the chair is already in a position to respond, "I already know about this. The decision is final," yet the student wouldn't be seen a fool since the chair knew because the student said as much, nor would the faculty be seen as "gossipy". Everyone wins here, no matter the decision. Most importantly, saying "but I would go no further" means that the student will accept the decision and not keep beating a dead horse, something many people do. Say right away that you're not like that.

How to deliver & respond:

Print on computer, no headers, only "Dear [PROF]" and a normal first-last name closing, sign with "Your student, [NAME]". You could make the entire request in handwriting, but DO NOT SIGN with the John Hancock! DO NOT EMAIL! Go in person, at least to deliver. Emails can be scary, especially anyone watching the news lately. Emails are convenient in daily life, but in conflict they are limited and lazy—can't solve conflict. Take time to deliver a note in person, be soft, friendly, informal, "via memo"—all these things add a pinch of kindness and a dash of diplomacy—things this situation needs all it can get of. Everyone can save face by this being informal. But, having it on paper, the prof can go directly to the chair and ask for advice, having the options of doing so formally or informally; we want that. Administrations should have the power to administer, and in administration do everything in writing. Respect administration and administration will respect you.

The student could drop it in the prof's mailbox or pin it to a board outside the office, whatever works. If delivered in person, be charming and humble and thankful. Even if the prof denies the request, be thankful for the learning opportunity, sit in the front row, and take double notes the rest of the semester. The best argument is "hard work" and could result in the grades not being lowered, even if the prof says no at first. Kindness and respect melts hearts.

Final thoughts:

Remember, profs are humans who deserve attention, even in survey lecture halls. They genuinely want students to learn. Their strange rules often come as a way of trying their best to help students learn what they will need.

Administrations are made of rules and respect hierarchies by definition; bucking against either will only cause brain damage.

Being a sesquipedalian is actually a good idea because academic journals are the sacred texts of academia; when in Rome... The key is to not use big words that confuse meaning because they aren't needed. Though it could be toned-down, that's not the case here.

Lastly, even in admitting wrong—the student should don the dunce cap here, but do so thankfully and respectably—NEVER, NEVER, NEVER do this: "I'm right because... but I'm sorry and you're right." Don't be a wet noodle; stand up and act like you have a spine, say "I need to act respectable by respecting the prof!" What good prof could resist the urge to honor that! But, that self-justify-then-roll-over approach is Satir's Blamer-Placater Distracter Mode and is half a penny shy of a formal request for a public beating.

In school, the purpose is to learn. So, prove that you're good in school by proving that you are learning. Learning is your best defense and work demonstrated is its best evidence.

Depending on your location, it may be illegal to use attendance to affect grading without a proper justification of why (and when) it is necessary to demand the attendance. One location where this would be illegal: the Netherlands.

People here are entering in complexe debates about the ethics or this or that...

She marked you as absent, were you and can you prove it ? That the only important thing here and the only thing you should bring up.

She is the one that will look stupid when she'll explain that she marked you absent because you were reading. Moreover if she can't prove that you were reading materials from another course.

Your entry level engineering course does have attendance requirements. Those rules were stated before you took the course. It does not matter whether you think the rules are silly or whether you think like I do that such rules are for children.

Do not take it further. It just turns up to the course. Going by what you have stated the professor is a bit precious which makes this likely to backfire on you. Maybe your so-called precious professor does not make the attendance rules either. Why should you expect her to say that you were there when you were not with the program? What if there were some safety aspects that students had to learn? These days with more internal assessment there is a greater correlation between being bad in class and getting bad grades.