On DNA Signatures, Their Dual-Use Potential for GMO Counterfeiting, and a Cyber-Based Security Solution

Abstract

This study investigates the role and functionality of special nucleotide sequences ("DNA signatures") to detect the presence of an organism and to distinguish it from all others. After highlighting vulnerabilities of the prevalent DNA signature paradigm for the identification of agricultural genetically modified (GM) organisms it will be argued that these so-called signatures really are no signatures at all - when compared to the notion of traditional (handwritten) signatures and their generalizations in the modern (digital) world. It is suggested that a recent contamination event of an unauthorized GM Bacillus subtilis strain (Paracchini et al., 2017) in Europe could have been-or the same way could be - the consequence of exploiting gaps of prevailing DNA signatures. Moreover, a recent study (Mueller, 2019) proposes that such DNA signatures may intentionally be exploited to support the counterfeiting or even weaponization of GM organisms (GMOs). These concerns mandate a re-conceptualization of how DNA signatures need to be realized. After identifying central issues of the new vulnerabilities and overlying them with practical challenges that bio-cyber hackers would be facing, recommendations are made how DNA signatures may be enhanced. To overcome the core problem of signature transferability in bioengineered mediums, it is necessary that the identifier needs to remain secret during the entire verification process. On the other hand, however, the goal of DNA signatures is to enable public verifiability, leading to a paradoxical dilemma. It is shown that this can be addressed with ideas that underlie special cryptographic signatures, in particular those of "zero-knowledge" and "invisibility." This means more than mere signature hiding, but relies on a knowledge-based proof and differentiation of a secret (here, as assigned to specific clones) which can be realized without explicit demonstration of that secret. A re-conceptualization of these principles can be used in form of a combined (digital and physical) method to establish confidentiality and prevent un-impersonation of the manufacturer. As a result, this helps mitigate the circulation of possibly hazardous GMO counterfeits and also addresses the situation whereby attackers try to blame producers for deliberately implanting illicit adulterations hidden within authorized GMOs.

Keywords: DNA signatures; GMO counterfeiting; bio-cryptanalysis; bio-cyber hacker; cryptographic applications; cyberbiosecurity; insecure channel; knowledge-based methods.

Figure 1

Major shortcomings of DNA signatures compared to traditional and cryptographic signatures. Traditionally, a number of security properties were obtained by sending a message concealed from outside manipulations, in form of sealed envelopes with signatures. This approach helped to ensure integrity (content of the message), its authenticity (sender and receiver), and confidentiality (the content is kept from access and alterations through unauthorized third parties). Similar features can be obtained by cryptographic signatures, by applying a mathematical algorithm (“signing”) to some fixed piece of information (“the message”). Importantly, any alterations to “the message” would not only be detected, but would invalidate the signature. The task of signing biologic entities is significantly more complex. This figure summarizes the critical vulnerabilities identified in the text (see section 3.2).

Figure 2

Herein, unrecognized risks involving counterfeiting attacks are identified that rely on the intentional misuse of prevailing DNA signatures (section 3). Although no such GMO counterfeit is confirmed in circulation, a recent B2 contamination event in Europe (Paracchini et al., 2017) demonstrates that these risks need to be taken seriously. Depending on the type of risk, different strategies need to be pursued. Steps toward realizing these goals are described in sections 4, 5.

Figure 3

The types of attacks involving GM plants as considered by Mueller (2019) (central part of the figure), roughly ordered from bottom to top relative to their risk-potential. Their impact is also hierarchical with risks at the lower level inherited at higher-levels. Herein, the focus is on the degree to which confidentiality and authenticity are violated (see section 4.2).

Figure 4

Herein, improvements of DNA signatures are obtained by utilizing cryptographic tricks that have proven useful for special cryptographic applications such as identification protocols and enhanced signatures (Menezes et al., ; Camenisch and Michels, ; Ateniese, ; El Aimani, ; Xia, 2013). At the core are (mathematical) interactive proof systems to demonstrate the (in)validity of a certain statement such as, “This is my personal PIN.” The significance of Zero-Knowledge (ZK) proofs lies in the fact that such systems can convince of the correctness of the statement without needing the involved parties to expose any details, such as, specifics of the PIN itself. ZK protocols can be overlaid with a feature that ensures authenticity of the originator of the statement or signature. When combined, this gives a powerful method to verify signatures while at the same time preventing their transferability or misuse by unauthorized parties.

Figure 5

Summary of the proposed method to enhance DNA signatures. Signatures are represented and verified in two ways. One is digital and based on specific cryptographic signatures (section 5.1) by utilizing enhanced Zero-Knowledge (ZK) proofs of knowledge via a cryptographic “invisibility” property (Figure 4). The second part ties the actual (physical) GMO to the digital part and adds a physical “invisibility” feature. Consequently, it is possible to (1) Demonstrate genuineness of a legitimate signature (this can be done both physically and digitally), (2) Prevent counterfeiters from selling manipulated GMOs, and (3) Allows authentic producers to demonstrate that a falsely attributed (fabricated) GMO is not theirs. This step may require WGS and can only be performed by a TTP or competent enforcement authorities who can verify the secret assignment into “valid” or “dummy”.

Figure 6

The digital part of the enhanced DNA signature method utilizes special cryptographic signatures (sections 5.1, 5.3) whereby signature verification is accomplished via a protocol rather than verification of presence or absence of a certain sequence. This gives a high degree of security and can only be achieved by legitimate producers (or their proxies) who know the underlying secret used for computing these cryptographic signatures. Attackers are not able to mimic this process and therefore cannot distribute counterfeits of GMOs by trying to masquerade them as the original product (Figure 2).

Figure 7

Various types of DNA signatures as considered herein, from bottom to top with increasing levels of security. 1. Represents the existing DNA signature paradigm (e.g., Levine, 2004); 2. and 3. are described in Mueller et al. (2016), and 4. (section 5) is an extension of the cryptographic invisibility feature which is central to the underlying cryptographic part in Mueller et al. (2016). (Sign, Signature; Adv, Advantage; Disadv, Disadvantage; Confirm, Confirmation).