As you note, Cracked.com is promoting the most eye-catching interpretation of the evidence, rather than the most likely and rigorous interpretation. There isn't any evidence for pre-Columbian, trans-Atlantic or trans-Pacific trade in tobacco or coca.

There are two main sources for this persistent myth (which crops up pretty frequently as evidence for the really bad Afro-centric interpretations of world history). First, you have the mummy of Ramses II. In 1978, abundant tobacco pollen and leaf fragments were discovered in the body cavity of the mummy^1. Second, in 1992, Balabanova et al. published their results indicating showing the presence of nicotine in the hair, bones, and soft tissue of a number of mummies based on radioimmunoassay and gas chromatography^1. They also identified compounds associated with cocaine and marijuana subsequently.

In both cases, the preferred interpretation was that of transmission across the Atlantic or Pacific from the Americas and the use of tobacco historically by Egyptians. I'll outline several of the problems with this interpretation, including likely sources of contamination.

To begin with, let's address the utter lack of evidence in any other form that there was pre-Columbian trade in drugs between New and Old Worlds. As you note, we should see some evidence for this trade either on the Atlantic side or the Pacific side, but the evidence pops up conspicuously only in Egypt. Not only do we not have any evidence from elsewhere in the Old World of this trade, but aside from these mummies we have no evidence in Egypt aside from the botanical and chemical remains. No art depicts cigarettes, pipes, or any other smoking of tobacco (let alone cannabis), and the epigraphic and textual record indicate extensive use of a variety of medicinal and ritual plants, none of which match the description for coca or tobacco.

This is all without considering that it would be really exceptional for people to be trading just these two drugs across hemispheres, without a shred of any other evidence making it to either side of the world. No Egyptian art found on the east coast of North America or evidence for Old World crops in the New, let alone evidence for any other kind of trade in artifacts or botanical to the Old World. Why exclusively coca and tobacco?

As for the botanical and chemical evidence, there are a number of alternate explanations which fits better the vast preponderance of evidence that indicates no exchange between Egypt and the New World.

First of all, every basic archaeology course is going to teach you that the story of an artifact doesn't end when it is placed on a museum shelf. All sorts of natural and anthropogenic processes will still have an impact on those objects even after they have been stored away. This is especially true of objects like many Egyptian mummies which where excavated in the late 19th and early 20th century, prior to modern standards of museum curation. Systematic contamination of a number of mummies is a very plausible explanation given this, and why I don't understand the argument about the sheer number of mummies identified with nicotine present as evidence against it being a matter of contamination. If all of those mummies where curated largely in the same way, systematic contamination of all of them is certainly possible.

Secondly, we need to carefully consider what the evidence actually tells us. While the presence of macro- and micro-botanical remains (like the leaf fragments and pollen in the body cavity of Ramses II) doesn't suggest use during life, and at best indicates use during the mummification or burial processes, even the chemical evidence from Balabanova et al. needs to be carefully considered. While the easiest interpretation of chemicals associated with cannabis, tobacco, and cocaine being identified in the soft tissue, hair, and bones of the mummies is that these drugs were used by these individuals during their life, there are alternate explanations.

To begin with, as Schafer points out in their response to Balabanova et al., that the identified chemicals would be stable within a mummified human body for over 3000 years is never established^2. I'm not familiar with the forensic toxicology of this, but we would need to establish that even given the unusual circumstances of mummification that these chemicals would be at all identifiable in any significant quantity after so long a time. This is especially so given their storage conditions after dis-entombment which may have aided in the breakdown of these drug compounds (due to increased oxygen). Additionally, again as noted by Schafer, we need to establish that the presence of the compounds in the soft tissue, hair, and bones is a product of use during life rather than use during embalming or some later contamination of the body. Perhaps by demonstrating differential quantities of the chemical compounds in parts of the hair at different distances from the scalp, rather than uniform quantities^3.

Finally, and most importantly, we need to consider the possibility of contamination in the 19th and 20th century in whatever museums and storage facilities these mummies where housed in. It has been suggested that the macro-botanical tobacco remains in Ramses II may have been modern snuff introduced into the body, though that explanation does not account for the tobacco pollen necessarily. However, the pollen may also be the product of a number of chamomile plants native to the Old World that may have been used historically in the embalming process^4. However, these plants were also used as an insecticide historically.

Similarly, tobacco is notable as a natural insecticide and was historically known to be such. Use as an insecticide in the embalming process was an original interpretation of the Ramses II tobacco, but use as part of modern museum conservation of the mummies is a much more probable source of the nicotine. Likewise for the examples studied by Balabanova, from Egypt and Eurasia. Control of insects is an important component of conservation practices, and Buckland and Panagiotakopulu point at textual evidence of tobacco being used as an insecticide in museum contexts from the late 19th and early 20th centuries^5. A lack of good object biographies for these mummies means we can't confirm this interpretation, but it is far more in line with existing evidence than is the use of ancient Egyptian tobacco.

We also can't discount the possibility that recreational drug use by curation staff at the turn of the century could have also contributed to the contamination, particularly the introduction of cocaine. While it might seem slightly absurd, the sensitivity of the techniques used to identify these trace amounts of drug compounds can potentially make them sensitive to environmental contamination, even from something as simple as smoking. While they use a different trace element technique (and so the sensitivity may be different), the recent study by Crown et al. to identify caffeine and theobromine (a compound in chocolate) in ceramics from the U.S. Southwest required that their analysts wear masks, gloves, and gowns in order to avoid contamination^6. Likewise, they were required to avoid bringing any caffeinated drinks into the lab. Even these minor sources of contamination were shown to be a possible source of contamination in the elemental tests, especially over the course of a number of years in a museum context. Keep in mind that this is all due to the sensitivity of the elemental analyses used, and the techniques used to identify the nicotine in the bodies may be less sensitive to such trace contamination.

In summary, the preponderance of evidence (and lack thereof) strongly indicates that the presence of these New World drugs in Egyptian mummies is the result of contamination in museum and other contexts from the last two centuries. The chemical analyses are hardly smoking guns, and the complete lack of any other evidence for such exchange across the hemispheres (or in any goods other than coca and tobacco) means that trade is a fairly preposterous explanation for the presence of these drug compounds on the mummies.

Edit: Grammar and typos.

^1 Buckland and Panagiotakopulu 2001: 550

^2 Hertting et al. 1993: 244

^3 Ibid., 243

^4 Buckland and Panagiotakopulu 2001: 552-553.

^5 Ibid., 553-554.

^6 Crown et al. 2015: 11436-11437.

Sources:

• Buckland, P.C. and E. Panagiotakopulu. 2001. Rameses II and the Tobacco Beetle. Antiquity, 75(289):549-556.

• Crown, Patricia L., Jiyan Gu, W. Jeffrey Hurst, Timothy J. Ward, Ardith D. Bravenec, Syed Ali, Laura Kebert, Marlaina Berch, Erin Redman, Patrick D. Lyons, Jamie Merewether, David A. Phillips, Lori S. Reed, and Kyle Woodson. 2015. Ritual drinks in the pre-Hispanic US Southwest and Mexican Northwest. PNAS, 112(37):11436-11442.

• Hertting, G., N. D. Philip McIntosh, and F. Parsche. 1993. Briefe An Die Herausgeber: Responding to First identification of drugs in Egyptian mummies. Naturwissenschaften, 80(6):243-246.