The first computer I used was a PDP-8 clone, which was a very primitive machine by today's standards - it only had 4k words of RAM (hand-made magnetic core memory !) - you could actually do simple programming tasks (such as short sequences of code to load software from paper tape) by entering machine code directly into memory by flipping mechanical switches on the front panel of the machine for individual bits (for data and memory addresses)

You could also write assembly code on paper, and then convert it into machine code by hand, and manually punch the resulting code sequence onto paper tape to then load into the machine (we had a manual paper punching device for this purpose)

Even with only 4k words of RAM, there were actually multiple assemblers and even compilers and interpreters available for the PDP-8 (FOCAL, FORTRAN, PASCAL, BASIC) - we only had a teletype interface (that printed output on paper), no monitor/terminal, so editing code on the machine itself was challenging, although there was a line editor which you could use, generally to enter programs you wrote on paper beforehand.

Writing assembly code is not actually the same as writing straight machine code - assemblers actually do provide a very useful layer of abstraction, such as function calls, symbolic addressing, variables, etc. - instead of having to always specify memory locations, you could use names to refer to jump points/loops, variables, functions, etc. - the assembler would then convert those into specific addresses as needed, so a small change of code or data structures wouldn't require huge manual process of recalculating all the memory locations as a result, it's all done automatically by the assembler.

So yeah, writing assembly code is still a lot easier than writing direct machine code - even when assembling by hand, you would generally start with assembly code, and just do the extra work that an assembler would do, but by hand.

Yes, you can code in machine code. I did it as part of my CS Degree. In our textbook was the manual for the particular ARM processor we coded for, that had every processor-specific command. We did that for a few of the early projects in the course, then moved onto Assembly, then C.

Assembly effectively is coding in binary. Been a long time since I've looked at it, but you'd basically just be recreating the basic assembly commands anyway.

I guess you could try flipping individual transistors with a magnet or an electron gun or something if you really want to make things difficult.

If you actually want to one-up assembly coders, then you can try designing your own processor on breadboard and writing your own machine code. Not a lot of easy ways to get into that, but there's a couple of turbo dorks on YouTube. Or you could just try reading the RISC-V specification.

But even then, you're following in someone else's tracks. I've never seen someone try silicon micro-lithography in the home lab, so there's an idea. Or you could always try to beat the big corps to the punch on quantum computing.

You can code in binary, but the only thing you'd be doing is frustrating yourself. We did it in the first week of computer science at the university. Assembly is basically just a human readable form of those instructions. Instead of some opcode in binary you can at least write "add", which makes it easier to see what's going on. The binary machine code is not some totally other language than what is written in the assembly code, so writing in binary doesn't really provide any more control or benefit as far as I'm aware.

All those assembly language instructions are just mnemonics for the actual opcodes. IIRC, on the 6502 processor family, JSR (Jump to SubRoutine) was hex 20, decimal 32. So going deeper would be really limited to not having access to the various amenities provided by assembler software and writing the memory directly. For example:

I started programming using a VIC-20. It came with BASIC, but you could have larger programs if you used assembly. I couldn't afford the assembler cartridge, so I POKED the decimal values of everything directly to memory. I ended up memorizing some of the more common opcodes. (I don't know why I was working in decimal instead of hex. Maybe the text representation was, on average, smaller because there was no need of a hex symbol. Whatever, it doesn't matter...)

VIC-BASIC had direct memory access via PEEK (retrieve value) and POKE (set value). It also had READ and DATA statements. READ retrieved values from the comma-delimited list of values following the DATA statement (usually just a big blob of values as the last line of your program).

I would write my program as a long comma-delimited list of decimal values in a DATA statement, READ and POKE those values in a loop, then execute the resulting program. For small programs, I just saved everything as that BASIC program. For larger programs, I wrote those decimal values to tape, then read them into memory. That let me do a kind of modular programming by loading common functions from tape instead of retyping them.

I was in the process of writing my own assembler so that I could use the mnemonics directly when I got my Apple //c. More memory and the availability of quite a few high level languages derailed me and I haven't touched assembly since.

Re: Coding in binary. It makes no difference. Your assembly is binary, just represented in a more human readable form when writing it in assembly.

Re: Manual interaction. Sure there's plenty of old computers where you can flip switches to input instructions or manipulate registers (memory on the cpu). But this is not much different from using assembly instructions except you're doing it live.

You can also create purpose built processors which might be what you mean? Generally this isn't too useful but sometimes it is. FPGAs are an example of doing this type of thing but using software to do the programming of the processor.

You could like make a simple accumulator machine out of logic gates and enter binary instructions expressed in hexadecimal into its register to program it, yeah, but it's not capable of all the operations of a computer. But yes the first programming was just op codes, switches flipped or punch cards, there was no assembly language. But assembly language is pretty much just mnemonics for operations and registers. Like I had to write a couple C programs in school and use GNU C compiler to disassemble them into x86 assembly and see what it was doing on that level, then we "wrote" some x86 assembly by copypasting a lot of instructions but its not that hard to make something that works in like x86 assembly or like Jasmin (Java virtual machine assembly language) if it's simple enough.

Assembly is binary