Technology in Star Trek is rather impressive. I think the transporter is one thing anyone, hard-core fan of the franchise or not, can come away with thinking, “I wish that were real!” Nearly instantaneous travel across long distances—who wouldn’t want that! (Check out other wish-it-were tech from sic-fi here.)
The idea behind it is the disassembling of a person (or item) at the molecular level (kind of like the TV room in Willy Wonka) and transmitting them electronically over a distance. It’s basically like faxing yourself. Besides possible horrific results, like in the 1958 film The Fly, the transporter raises ethical questions, treated powerfully in The Prestige. Remember, fax machines copy a page and transmit it electronically to another place, where it is copied. The original document never travels, so you’d basically be making a copy of yourself. But more than that, it assumes that all there is to a person is matter.
I’m not talking about the mind per se so much as the notion of the human soul. In some sense, memory and personality are encoded in neural pathways and [insert impressive brain words], but concept of the soul is not connected with any specific organ or part of the body. The implication of Star Trek’s transporter, then, is that there is no soul.
Star Trek, to my knowledge (which is fairly extensive with regard to Star Trek: the Next Generation, it’s movies, and Star Trek: Voyager, and adequate among the other series), never address the state of religion among humanity. (They also never address waste management and toilets, but that’s another conversation entirely.) They encounter the belief systems of alien races frequently, but I cannot remember a single instance in which they directly address the belief system(s) still practiced among humans. There are weddings and funerals in the show, and both these types of ceremonies often contain religious language or implication—but no.
Are we to assume that since none of the human characters ever practice any religious observance, their entire society is homogeneously atheistic? That’s patently absurd; we might as well assume that humans have evolved past the need to void their bladders because the show never even shows a toilet in crew members’ quarters. No, my guess is that the writers wished to avoid alienating parts of their fan base. Regardless of the intention, the existence and extensive use of transporter technology in Star Trek seems to imply a stance on that worldview. That mankind does not possess a soul and can therefore be disassembled and reassembled somewhere else.
Don’t check your brain at the door.