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It is generally accepted that pork and chicken must be cooked completely (unless put through a strong curing process) while certain cuts of beef and lamb can be served on the rare side. Why is this?

Are particular bacteria populations present in some animals but can't survive in others? What is the inherent differences between these animals that makes the difference when eating? How can I objectively decide if it is safe to eat something partially on the rare side that does not involve simply trusting the "common knowledge" of the more experienced.

(Don't get me wrong - I appreciate any and all advice that I get from anyone who is more experienced than I am in anything, but I'd like to know how they came to their conclusions).

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Add-on to your question: How come duck is always served medium? One would think it would be similar to chicken... –  uvesten Jun 11 '12 at 14:52
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Beef (and Lamb): The surface of beef is often contaminated with pathogens such as e-coli. However, the meat is very dense and the bacteria cannot migrate from the surface into the flesh. Therefore, beef is safe to consume once the external temperature exceeds, 160 degrees F. The internal uncontaminated meat is safe to eat raw.

Pork: Like beef the surface of pork needs to be fully cooked. Unlike beef, pigs harbor a parasitic roundworm called Trichinella spiralis. Infection with the worm is called trichinosis and can be fatal. This worm is killed when the flesh reaches 150 degrees F and is held there for several minutes. Therefore pork is safe to consume when cooked to medium. (Commercial pork in North America almost never has the roundworm present. Almost every case (all?) of trichinosis in the last 15-20 years have come from undercooked wild boar or bear meat). Trichinella spiralis can also be killed by freezing (time and temperature dependent).

Chicken: Almost all chickens have Salmonella or Campylobacter present on the surface (at least). However, chickens have a less dense flesh than pigs, sheep or cows. Therefore, the bacteria can migrate deep into the flesh. Also, the processing of chickens is much more invasive than the previously mentioned animals which also means the interior meat can get contaminated. This means the meat must be cooked to well done throughout.

Duck: With duck it seems to come down to a matter of processing verses chicken. Also, they are raised in a much less confined manor, which helps prevent the spread of pathogens. There is still a chance of getting a salmonella infection from undercooked duck but cooking the breast well done basically ruins it, so people take the (small) risk.

Ground meat: Grinding meat, by its nature, implies the surface and the interior is mixed. Therefore, one must assume the meat is fully contaminated and must be entirely cooked to well done.

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Interesting info, I never heard of these things. Do you have more in-depth links for "chicken meat is less dense"? Also, the sentence "almost all chickens have salmonelly or campylobacter" sounds improbable, do you have a source? (I agree that campylobacter is a common bacterium, but I would expect it on other meats too. Salmonella infected chickens are not that common, as far as I know). –  rumtscho Jun 11 '12 at 20:50
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Bacteria found in 83% of chickens (usatoday.com/news/health/2006-12-04-chicken-bacteria_x.htm). 37%–51% Campylobacter in Canada (cmaj.ca/content/177/6/570.full) –  Swoogan Jun 12 '12 at 3:57
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Chicken meat is less dense than beef or pork (busycooks.about.com/od/cookinglessons/a/foodsafety.htm). Not the most authoratative source, but I could not find anything else that explained why cooking the surface of chicken meat would not follow the same reasoning as beef. –  Swoogan Jun 12 '12 at 4:01
    
I suspect it's not really "density" but fat content; ducks are fairly fatty and fat tends to protect pretty well against bacteria, but chicken is very lean. Farming/confinement and simple popularity may also be a part of it; I think duck is a lot less likely to be contaminated, and being less frequently eaten, there's no reason for farmers to try to mass-produce it on the same scale as chicken. –  Aaronut Jan 14 '13 at 0:25
    
I'm leaning more toward it being how deeply the quill of the feathers penetrate the flesh during processing. That coupled with the availability of pathogens on the surface to "inject" into the meat. –  Swoogan Jan 15 '13 at 22:52
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Traditionally pork and chicken have been more disease ridden, carriers of parasites, and have high surface bacteria counts. So thorough cooking has always been advised

If you know the source of the pork or chicken, you can cook it rare too. Some cultures will eat it raw

It all comes down to how much you know and trust your meat provider

There are also doggy beef and lamb suppliers out there, that you would be best to thoroughly cook beef and lamb from them too

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Chicken meat and eggs carry the risk of salmonella. Salmonella are bacteria which cause severe symptoms, and can even end in death, unlike other, milder types of food poisoning. They are also hardy bacteria, and the temperature needed for them to die quickly is above the temperature for medium rare. In theory, you could eat poultry medium rare if you ensure that it has stayed at the lower temperature for a sufficiently long time, but the relationship is not linear, and if you are not well acquainted with the times needed and don't use a thermometer consequently, it is safer to heat it to well done.

Pork is known as a possible source of trichinosis, which is caused by a parasite. It also needs very high temperatures to die. Systematic veterinary control has almost eradicated trichinosis in developed countries for commercial pork, so eating pork at medium rare is considered reasonably safe today. Care should still be taken if you are preparing wild boar as a significant risk of trichinosis remains in game hogs. (Small slaughter houses and butcher shops may offer pork from wild boars in (following) hunting season.)

Other meats have their own share of nasties, especially E.coli - they are usually just unpleasant, but some strains can be very dangerous, like the one in Germany last summer. Be warned that with modern safety procedures, you are more likely to get your food poisoning from produce (because it is often not heated, but eaten as salads, etc.) than from meat. So don't forget to wash your veggies.

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Trichinosis strains found in pork can be killed by freezing, too. And it dies fairly quickly (<3min) at 136°F. See law.cornell.edu/cfr/text/9/318.10 or –  derobert Jun 11 '12 at 14:38
    
Why is trichinosis not present in cattle? Is it because they can die from it where as hogs can withstand it and pass it on to their predators? Or what about salmonella in other birds besides chicken? Is it not present in ducks as well? I know some of these questions will start to border on biology... but I was wondering if anyone had knowledge in this area. I understand if that is an unreasonable request given the scope of this site. –  Jon Jun 11 '12 at 19:19
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It is normal for parasites to have a very specific relationship with their host. Trichinosis worms can't live in anything but pigs, so beef is safe from it. As for salmonella, it can live in many animals. I don't know why it is usually connected with chickens, probably historically this has been the most common source of outbreaks. –  rumtscho Jun 11 '12 at 19:27
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