Ciro Santilli @cirosantilli 37

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Basal (phylogenetics)  Updated 2025-05-23  +Created 1970-01-01

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When a characteristic is basal, it basically means the opposite of it being polyphyletic.

E.g. monotremes laying eggs did not evolve separately after function loss, it comes directly from reptiles.

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Drug  Updated 2025-05-23  +Created 1970-01-01

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For Ciro Santilli's unimpressive drug experiences see: Section "Ciro Santilli's drug experiences".

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Electronic oscillator  Updated 2025-05-23  +Created 1970-01-01

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Something where DC voltage comes in, and a periodic voltage comes out.

Video 1.

Oscillators: RC, LC, Crystal by GreatScott! (2015)

Source. Good video. Contains actual breadboard experiments on oscilloscope and circuit diagrams

youtu.be/eYVOdlK15Og?t=66 RC oscillator on breadboard. Produces rectangular wave. Mentions popular integrated circuit that does it: 555 timer IC.
youtu.be/eYVOdlK15Og?t=175 LC oscillators allows for higher frequencies. Produces sinusoidal output on MHz range. Uses an amplifier to feed back into input and maintain same voltage. Hard to make reliably on breadboard.
youtu.be/eYVOdlK15Og?t=315 crystal oscillator. Mentions it acts like an LC oscillators. Shows and equivalent model. Wish he had talked more about them. You need support components around it: similarly to the LC case, the amplifier is generally not packaged in.

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Quote by Richard Feynman  Updated 2025-05-23  +Created 1970-01-01

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Sponsor Ciro Santilli's work on OurBigBook.com / Updates  Updated 2025-05-23  +Created 1970-01-01

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System of partial differential equations  Updated 2025-05-23  +Created 1970-01-01

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In many important applications, what you have to solve is not just a single partial differential equation, but multiple partial differential equations coupled to each other. This is the case for many key PDEs including:

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ELF Hello World Tutorial / .data section  Updated 2025-05-23  +Created 1970-01-01

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.data is section 1:

00000080  01 00 00 00 01 00 00 00  03 00 00 00 00 00 00 00  |................|
00000090  00 00 00 00 00 00 00 00  00 02 00 00 00 00 00 00  |................|
000000a0  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000b0  04 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|

80 0: sh_name = 01 00 00 00: index 1 in the .shstrtab string table
Here, 1 says the name of this section starts at the first character of that section, and ends at the first NUL character, making up the string .data.
.data is one of the section names which has a predefined meaning according to www.sco.com/developers/gabi/2003-12-17/ch4.strtab.html:
These sections hold initialized data that contribute to the program's memory image.

80 4: sh_type = 01 00 00 00: SHT_PROGBITS: the section content is not specified by ELF, only by how the program interprets it. Normal since a .data section.
80 8: sh_flags = 03 7x 00: SHF_WRITE and SHF_ALLOC: www.sco.com/developers/gabi/2003-12-17/ch4.sheader.html#sh_flags, as required from a .data section
90 0: sh_addr = 8x 00: TODO: standard says:
If the section will appear in the memory image of a process, this member gives the address at which the section's first byte should reside. Otherwise, the member contains 0.
but I don't understand it very well yet.
90 8: sh_offset = 00 02 00 00 00 00 00 00 = 0x200: number of bytes from the start of the program to the first byte in this section
a0 0: sh_size = 0d 00 00 00 00 00 00 00
If we take 0xD bytes starting at sh_offset 200, we see:
```
00000200  48 65 6c 6c 6f 20 77 6f  72 6c 64 21 0a 00        |Hello world!..  |
```
AHA! So our "Hello world!" string is in the data section like we told it to be on the NASM.
Once we graduate from hd, we will look this up like:
```
readelf -x .data hello_world.o
```
which outputs:
```
Hex dump of section '.data':
  0x00000000 48656c6c 6f20776f 726c6421 0a       Hello world!.
```
NASM sets decent properties for that section because it treats .data magically: www.nasm.us/doc/nasmdoc7.html#section-7.9.2
Also note that this was a bad section choice: a good C compiler would put the string in .rodata instead, because it is read-only and it would allow for further OS optimizations.
- a0 8: sh_link and sh_info = 8x 0: do not apply to this section type. www.sco.com/developers/gabi/2003-12-17/ch4.sheader.html#special_sections
- b0 0: sh_addralign = 04 = TODO: why is this alignment necessary? Is it only for sh_addr, or also for symbols inside sh_addr?
- b0 8: sh_entsize = 00 = the section does not contain a table. If != 0, it means that the section contains a table of fixed size entries. In this file, we see from the readelf output that this is the case for the .symtab and .rela.text sections.

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Elliptic curve primality  Updated 2025-05-23  +Created 1970-01-01

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Polynomial time for most inputs, but not for some very rare ones. TODO can they be determined?

But it is better in practice than the AKS primality test, which is always polynomial time.

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PayPal founder  Updated 2025-05-23  +Created 1970-01-01

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Search engine optimization  Updated 2025-05-23  +Created 1970-01-01

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Taylor series  Updated 2025-05-23  +Created 1970-01-01

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An overview of recent non-standard Bitcoin transactions by 0xB10C  Updated 2025-05-23  +Created 1970-01-01

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b10c.me/observations/09-non-standard-transactions/

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Asthma  Updated 2025-05-23  +Created 1970-01-01

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ELF Hello World Tutorial / Executable hd  Updated 2025-05-23  +Created 1970-01-01

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Running:

hd hello_world.out

gives:

00000000  7f 45 4c 46 02 01 01 00  00 00 00 00 00 00 00 00  |.ELF............|
00000010  02 00 3e 00 01 00 00 00  b0 00 40 00 00 00 00 00  |..>.......@.....|
00000020  40 00 00 00 00 00 00 00  10 01 00 00 00 00 00 00  |@...............|
00000030  00 00 00 00 40 00 38 00  02 00 40 00 06 00 03 00  |....@.8...@.....|
00000040  01 00 00 00 05 00 00 00  00 00 00 00 00 00 00 00  |................|
00000050  00 00 40 00 00 00 00 00  00 00 40 00 00 00 00 00  |..@.......@.....|
00000060  d7 00 00 00 00 00 00 00  d7 00 00 00 00 00 00 00  |................|
00000070  00 00 20 00 00 00 00 00  01 00 00 00 06 00 00 00  |.. .............|
00000080  d8 00 00 00 00 00 00 00  d8 00 60 00 00 00 00 00  |..........`.....|
00000090  d8 00 60 00 00 00 00 00  0d 00 00 00 00 00 00 00  |..`.............|
000000a0  0d 00 00 00 00 00 00 00  00 00 20 00 00 00 00 00  |.......... .....|
000000b0  b8 01 00 00 00 bf 01 00  00 00 48 be d8 00 60 00  |..........H...`.|
000000c0  00 00 00 00 ba 0d 00 00  00 0f 05 b8 3c 00 00 00  |............<...|
000000d0  bf 00 00 00 00 0f 05 00  48 65 6c 6c 6f 20 77 6f  |........Hello wo|
000000e0  72 6c 64 21 0a 00 2e 73  79 6d 74 61 62 00 2e 73  |rld!...symtab..s|
000000f0  74 72 74 61 62 00 2e 73  68 73 74 72 74 61 62 00  |trtab..shstrtab.|
00000100  2e 74 65 78 74 00 2e 64  61 74 61 00 00 00 00 00  |.text..data.....|
00000110  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00000150  1b 00 00 00 01 00 00 00  06 00 00 00 00 00 00 00  |................|
00000160  b0 00 40 00 00 00 00 00  b0 00 00 00 00 00 00 00  |..@.............|
00000170  27 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |'...............|
00000180  10 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000190  21 00 00 00 01 00 00 00  03 00 00 00 00 00 00 00  |!...............|
000001a0  d8 00 60 00 00 00 00 00  d8 00 00 00 00 00 00 00  |..`.............|
000001b0  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001c0  04 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001d0  11 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
000001e0  00 00 00 00 00 00 00 00  e5 00 00 00 00 00 00 00  |................|
000001f0  27 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |'...............|
00000200  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000210  01 00 00 00 02 00 00 00  00 00 00 00 00 00 00 00  |................|
00000220  00 00 00 00 00 00 00 00  90 02 00 00 00 00 00 00  |................|
00000230  08 01 00 00 00 00 00 00  05 00 00 00 07 00 00 00  |................|
00000240  08 00 00 00 00 00 00 00  18 00 00 00 00 00 00 00  |................|
00000250  09 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
00000260  00 00 00 00 00 00 00 00  98 03 00 00 00 00 00 00  |................|
00000270  4c 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |L...............|
00000280  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000290  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002a0  00 00 00 00 00 00 00 00  00 00 00 00 03 00 01 00  |................|
000002b0  b0 00 40 00 00 00 00 00  00 00 00 00 00 00 00 00  |..@.............|
000002c0  00 00 00 00 03 00 02 00  d8 00 60 00 00 00 00 00  |..........`.....|
000002d0  00 00 00 00 00 00 00 00  01 00 00 00 04 00 f1 ff  |................|
000002e0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002f0  11 00 00 00 00 00 02 00  d8 00 60 00 00 00 00 00  |..........`.....|
00000300  00 00 00 00 00 00 00 00  1d 00 00 00 00 00 f1 ff  |................|
00000310  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000320  00 00 00 00 04 00 f1 ff  00 00 00 00 00 00 00 00  |................|
00000330  00 00 00 00 00 00 00 00  2d 00 00 00 10 00 01 00  |........-.......|
00000340  b0 00 40 00 00 00 00 00  00 00 00 00 00 00 00 00  |..@.............|
00000350  34 00 00 00 10 00 02 00  e5 00 60 00 00 00 00 00  |4.........`.....|
00000360  00 00 00 00 00 00 00 00  40 00 00 00 10 00 02 00  |........@.......|
00000370  e5 00 60 00 00 00 00 00  00 00 00 00 00 00 00 00  |..`.............|
00000380  47 00 00 00 10 00 02 00  e8 00 60 00 00 00 00 00  |G.........`.....|
00000390  00 00 00 00 00 00 00 00  00 68 65 6c 6c 6f 5f 77  |.........hello_w|
000003a0  6f 72 6c 64 2e 61 73 6d  00 68 65 6c 6c 6f 5f 77  |orld.asm.hello_w|
000003b0  6f 72 6c 64 00 68 65 6c  6c 6f 5f 77 6f 72 6c 64  |orld.hello_world|
000003c0  5f 6c 65 6e 00 5f 73 74  61 72 74 00 5f 5f 62 73  |_len._start.__bs|
000003d0  73 5f 73 74 61 72 74 00  5f 65 64 61 74 61 00 5f  |s_start._edata._|
000003e0  65 6e 64 00                                       |end.|
000003e4

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Anime  Updated 2025-05-23  +Created 1970-01-01

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Computer hardware component type  Updated 2025-05-23  +Created 1970-01-01

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Modular multiplication  Updated 2025-05-23  +Created 1970-01-01

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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it / PCR verification with gel electrophoresis  Updated 2025-05-23  +Created 1970-01-01

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Biology experiments are hard, and so they go wrong, a lot.

For this reason, it is wise to verify that certain steps are correct whenever possible.

And so this is the first thing we did on the second day!

Gel electrophoresis separates molecules by their charge-to-mass ratio. It is one of those ultra common lab procedures!

This allows us to determine how long are the DNA fragments present in our solution.

Since we know that we amplified the 16S regions which we know the rough size of (there might be a bit of variability across species, but not that much), we were expecting to see a big band at that size.

And that is exactly what we saw!

First we had to prepare the gel, put the gel comb, and pipette the samples into wells present in the gel:

To see the DNA, we added ethidium bromide to the samples, which is a substance that that both binds to DNA and is fluorescent.

Because it interacts heavily with DNA, ethidium bromide is a mutagen, and the biology people sure did treat the dedicated electrophoresis bench area with respect! Figure 4. "Gel electrophoresis dedicated bench area to prevent ethidium bromide contamination.".

The UV transilluminator we used to shoot UV light into the gel was the Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator. The fluorescent substance then emitted a light we can see.

As barely seen at Figure 8. "Fischer Scientific UVP LM-26E Benchtop 2UV Transilluminator illuminated gel." due to bad photo quality due to lack of light, there is one strong green line, which compared to the ladder matches our expected 16S length. What we saw it with the naked eyes was very clear however.

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Politics of the United States  Updated 2025-05-23  +Created 1970-01-01

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Real coordinate space of dimension three  Updated 2025-05-23  +Created 1970-01-01

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