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Replicators are used ubiquitously throughout the Star Trek universe to produce any material that the user desires - notably food and drink. On a starship, the crew's entire diet would consist of replicated food matter.

However, replicated matter is known for having innate flaws. This is why rare materials and living intelligent creatures cannot be stored and replicated at a whim - the matter involved is too complex. Yet in all matter, including that which is replicated for consumption, these atomic errors persist.

Has there ever been an instance of or suggestion that a diet of replicated food and drink may have an adverse effect on a person?

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    Good question. I like it. Disliking replicated food often seems to go hand-in-hand (story-wise) with being slightly outside the Federation's core philosophy. – Valorum Nov 8 '14 at 14:29
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    I've always thought that was the silliest thing on Star Trek... To make 1kg of cheese you would need to convert 1kg of antimatter to energy, then convert it back again to matter, why not just carry the cheese in the first place?? – Gaius Nov 10 '14 at 12:43
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    @Gaius - Because you can take that 1KG of raw matter and make anything from the menu, pharmaceuticals or clothing or machine parts. If you carry cheese, it needs to be refigerated and can only be used for one thing. – Valorum Nov 10 '14 at 13:26
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    And how much antimatter did it take for you to warp that extra kilogram of cheese across the galaxy? – Stephen Collings Nov 14 '14 at 17:23
  • @Gaius en.memory-alpha.org/wiki/Replicator The replicator appears to take existing matter and rearrange it to create the required item. I would assume that this means that it is more energy efficient. Matter is available in many forms from on-board waste recycling to sucking up hydrogen & dust from space. – Jaydee Dec 8 '14 at 15:59
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The short answer is no.

Nutrition :

Regarding the composition of replicated food, the TNG Technical Manual (considered to be a fully canon reference guide) specifically states that food replicators are capable of producing food molecules at sufficiently high fidelity to provide all needed sustenance with no adverse effects:

"As with all transporter-based replication systems, the food replicators operate at molecular resolution. Because of this, there are significant numbers of single-bit errors in the resulting replicated materials. These errors are not nutritionally significant (although some individuals do claim to be able to taste differences in certain dishes), but certain types of Altarian spices have shown a tendency to become mildly toxic when replicated, so their use is avoided in replicated dishes."

Miles O'Brien (a transporter and replicator specialist) casts scorn on his mother's prejudice that replicated food doesn't provide the same high quality nutrition:

KEIKO: She cooked?

O'BRIEN: She didn't believe in a replicator. She thought real food was more nutritious.

KEIKO: She handled real meat? She touched it and cut it?

O'BRIEN: Yeah, like a master chef. She was fantastic. Of course, I'll have to use the replicator, but I'll make something special for you tonight. You'll love it, I promise. - TNG : The Wounded

If anything (as we see in @Tritium21's answer) it's actually the opposite. The replicator allows you to artificially control the levels of fat, sugar and protein in your food and will actively resist you trying to make something damaging to your health:

TROI : And computer, I'd like a real chocolate sundae.

COMPUTER : Define "real" in context, please.

TROI : Real... not one of your perfectly synthesized, ingeniously enhanced imitations... real chocolate ice cream, real whipped cream...

COMPUTER : This unit is programmed to provide sources of nutritional value. Your request does not fall within current guidelines. - TNG : The Price

Taste

It's not uncommon for characters to disparage the taste of replicated food, but there's no indication in either the TV show or the other canon materials (writer's guides, technical manuals, etc) to suggest that replicated matter is actually bad for you.

WILDMAN: I thought you didn't use replicated vegetables when you're cooking. Always fresh, organic, from the airponic bay.

NEELIX: Well, the yields have been a little low lately. Normally, I would never dream of using synthesised veggies. - Voy : Deadlock

and

EDDINGTON: Replicator entree number one oh three. Curried chicken and rice with a side order of carrots. Or at least that's what they want us to believe. But you and I both know what we're really eating. Replicated protein molecules and textured carbohydrates.
SISKO: It's not that bad.

EDDINGTON: It may look like chicken, but it still tastes like replicated protein molecules to me.

SISKO: If you don't want it, don't eat it. - DS9: Blaze of Glory

and

JOSEPH [on monitor]: Whatever you do during the day is your business. But at dinner time, you better get yourself down to New Orleans. No son of mine is going to eat that replicated slop Starfleet calls food. Not if I have anything to say about it. - DS9: Homefront

and

SEYETIK:...Which reminds me, wait till you taste the food my wife has created for you. None of that replicated nonsense you're used to. No, every dish was prepared entirely by Nidell's own sweet hands. - Second Sight

and

SISKO: Maybe you need a vacation.

LEYTON: Mmm. Somehow replicated coffee never tastes this good. I'm afraid I owe you an apology, Ben. - Paradise Lost

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    I would also add another sort-of example to back you up on this. In one of the TNG novels where the next Enterprise is commanded by the crew of the starship caught in the temporal loop from one of the episodes, it makes a point that the captain insists on having a proper mess on board his ships because he doesn't believe for one second that the replicator food is either as tasty or as physically/emotionally fulfilling and nutritious. – Broklynite Nov 8 '14 at 18:29
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    @Richard: The quote about the Altarian spices being toxic seems like a counterexample. The short answer is yes. – ThePopMachine Nov 8 '14 at 19:02
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    @ThePopMachine - As you can see from the Troi quote, the machine will actively resist you making anything toxic or poisonous (such as hemlock, for example; en.memory-alpha.org/wiki/Nogatch_hemlock). The question wasn't whether you can override the controls to make something dangerous such as pharmaceuticals, it was whether a diet of replicated food is inherently bad for you. – Valorum Nov 8 '14 at 19:03
  • @Richard: Well the distinction between "Replicated food is identical" and "The replicator won't let you make anything dangerous" is pretty significant and should be highlighted. – ThePopMachine Nov 8 '14 at 19:07
  • @ThePopMachine - I haven't said that they're identical, just not damaging to health under normal circumstances. – Valorum Nov 8 '14 at 19:09
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Troi: ...And computer, I would like a real chocolate sundae

Computer: Define "Real" in context please

Troi: Real. Not one of your perfectly synthesized, ingeniously enhanced imitations. I would like real chocolate ice cream, real whipped cream...

Computer: This unit is programmed to provide sources of acceptable nutritional value. Your request does not fall within current guidelines. Please indicate whether you wish to override the specified program?

From TNG - The Price

As indicated from this dialog, replicated food is intended to be of superior nutrition than natural food. To clarify, a replicator will, by default, when asked for a menu item, produce one with better nutritional value than if produced traditionally - and this makes sense; the replicator has full control over the matter in a product, within a small margin for error, much smaller margin than the variance inherent to agriculture.

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    A very good example. You have my +1 – Valorum Nov 8 '14 at 18:33
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I can't top Richard's detailed answer, but wanted to add a little more flavour (bad pun, sorry) as to why people claim replicator food tastes so bad. Studies have shown the reason people believe airline food tastes bad is actually because their taste buds don't work as well in-flight. The combination of a dry atmosphere and cabin pressure interferes with the working of the taste bud, so things taste bad as a result. It's possible that the conditions on a space craft/station are not too dissimilar, so this could be the root of a lot of the perceptions people have around the taste of replicated food being different.

These stories get carried back by the crew/passengers and spread around their on-world families and friends and suddenly the myth is a common misconception and impossible to shake, and to some extent self-fulfilling (i.e. if you think it's going to taste bad before you eat it, you'll shape your experience somewhat). There was a recent story about Dutch food experts given McDonalds burgers but being told they were organic and they praised them, claiming they were much tastier than anything you'd find in McDonalds, so clearly perception plays a huge part in the taste of our food.

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    This is an interesting theory, but there already is a reason they might suspect the food tastes worse, or at least different. No cabin pressure issues need to be introduced to explain that. – Zibbobz Nov 10 '14 at 14:00
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The microbiome (the systems of bacteria that live inside us) is a recent discovery, and could be brought up if you are writing your own novel. A lifelong diet of 100% replicated food might not include those organisms. Health problems would certainly result from that, if it wasn't taken into consideration (maybe during the early days of replicator technology). The whole issue of "can replicators clone living organisms in my universe?" would have to come into play.

http://en.wikipedia.org/wiki/Microbiome

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    Replicators cannot create living stuff (at least not intentionally). It's one of their primary limitations. – Valorum Nov 9 '14 at 20:19
  • @Richard, I think that this exactly is the problem mentioned - replicated food may not be as nutritious for us, because it cannot contain probiotics. – yoniLavi Nov 10 '14 at 19:18
  • @yoniLavi - It's certainly possible that they're given intestinal flora at an early age (breast milk?) which then persists their whole life – Valorum Nov 10 '14 at 19:20

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