Then you can use an external EEPROM reader that can dump the contents, but is not capable of running the code.
The EEPROM is storage only; it's contents are loaded by the PC at boot. So if it is removed, there is no processing that an occur internally than can mask the data inside of it.
EDIT: Sorry for being unclear. I'm aware EEPROM can be overwritten. But presumably that requires special privileges, or a special circumstance (like the user physically holding some button on the motherboard during bootup, or something). The article isn't at all clear how it's possible to write a program that escalates its privileges to such an extent that it can then overwrite EEPROM. Is it really possible? How?
Electronically Erasable Read Only Memory
It's re-programmable (i.e. by re-flashing it).
edit: I should add that motherboard manufacturers could prevent this type of attack by "locking" the BIOS for flashing unless it was explicitly unlocked by changing a setting in the BIOS menu (some have this already, I believe). The problem at the moment is that the BIOS is writable at all times, even when the OS is running. This makes BIOS updates easier (i.e. you can make a Windows application that can do so, for example), but the problem is that this allows ANY process with Admin access to alter the BIOS as well.
I'm speechless that this horrible idea was ever taken seriously, much less implemented. That answers my question as to how a BIOS could become infected.
I'm seriously sitting here in shock. How could any hardware manufacturer think it was a good idea to let a userspace program permanently alter EEPROM, ever? One does not need to be very intelligent to realize hackers will hack that.
This brings us full circle to the original question, though: Did the security researcher write a program to dump the contents of EEPROM rather than desoldering the chips? if so, then he may have been hoodwinked by the virus.
Because most hardware manufactures are selling to consumers and not cypherpunks.
Is this different than getting a dump of the BIOS before flashing it? Are we talking about different chips on the motherboard?
The '80s solution to this problem was way easier, and it worked: a switch on the motherboard required physical access to the machine to flash its firmware.