Ahmed Aldeeb

Beyond End-To-End: unveiling the Quantum threat to Encryption

Computer Science, Editors Pick, Mathematics, Must Read, Technology / By

If you’ve ever used Whatsapp or Instagram to communicate with friends and family, you’d notice that the messages are “end-to-end encrypted”. Upon first notice, it sounds great. All your messages are safe and secure – you’d think. 

However, not every encryption method is created equal, and with the rise of cyberattacks and more sophisticated technology especially in the Quantum field, one must exercise caution when choosing the right tools to use. But to better understand the scale of this issue we must first address the mathematical operation that makes such risk feasible in the first place.

Shor’s algorithm poses a major threat to security provided by current industry-standard encryption methods like RSA and ECC which rely on the difficulty of factoring large integers for security. However this difficulty is limited to the classical world of computing, where operations would be trialed one by one until a solution is found (exponential time) making it almost impossible to decipher such encryption methods. On the other hand, a Quantum computer is able to simultaneously compute all the possible trials in a single iteration due to it being in a superposition of exponentially many states – achieving rapid polynomial time. In simpler terms, many of the “asymmetric” encryption methods are at risk.

Evidently, this causes a domino effect on Symmetric encryption methods, since most Symmetric keys are exchanged between users through an asymmetric exchange process, which could be compromised by Shor’s algorithm allowing potential decryption of all data encrypted with that key: including your texts and photos.

Whilst this threat isn’t currently feasible for ordinary individuals — since Quantum Computers are costly, sophisticated pieces of technology –  many countries and researchers are becoming increasingly aware of its uses and have created their own. Evidently, there is an imminent risk that Quantum threats may have the potential to escalate cyberattacks and transform the digital landscape as we know it. 

Moreover, some authorities and individuals are adopting a technique called “Harvest Now, Decrypt Later”: accumulating databases of encrypted information. In hopes, it could one day be decrypted with sufficiently powerful quantum computers. 

Evidently, many companies and researchers (including NIST) have taken measures to enhance encryption methods and implement Quantum safe or secure encryption in their communication protocols. One example, is the open-source messaging platform signal, which introduced the new PQXDH encryption protocol that claims to be quantum resistant to current advancements in the field of encryption: however, they claim that such technology must be upgraded as future findings and vulnerabilities may require additional security adjustments. If you wish to, the whitepaper for the encryption method can be accessed here.

Conclusion

Finally, we realised that such advancements pose a monumental risk to information security. Although it’s easy to be pessimistic about such advancements, I believe that it’s a step in the right direction towards safeguarding our digital security and communication. Therefore, as individuals and organisations alike we must take proactive measures:

  • Stay Informed: Keep abreast of developments in quantum computing and its implications for encryption. Awareness is key to making informed choices.
  • Quantum-Safe Encryption: Consider adopting encryption methods that are resilient to quantum attacks. New cryptographic standards, often referred to as Post-Quantum Cryptography (PQC), are being developed to address this specific concern.
  • Advancements in Technology: Support and invest in technologies that stay ahead of the curve (especially open-source projects), continually updating encryption methods to withstand emerging threats.

Sources

https://csrc.nist.gov/projects/post-quantum-cryptography/
https://statweb.stanford.edu/~cgates/PERSI/papers/MCMCRev.pdf
https://purl.utwente.nl/essays/77239/
https://ico.org.uk/for-organisations/uk-gdpr-guidance-and-resources/security/encryption/what-types-of-encryption-are-there/#:~:text=There%20are%20two%20types%20of,used%20for%20encryption%20and%20decryption.
https://signal.org/docs/specifications/pqxdh/

Quantum-Inspired AI model helps CRISPR Cas9 Genome Editing for Microbes

Artificial Intelligence, Biology, Biotech, Medicine, Science, Technology / By


A team of scientists at the Oak Ridge National Laboratory (ORNL), have embarked on a groundbreaking venture, leveraging quantum biology, artificial intelligence (AI), and bioengineering to revolutionize the effectiveness of CRISPR Cas9 genome editing tools. Their focus is on microbes, particularly those earmarked for modifications to produce renewable fuels and chemicals, presenting a unique challenge due to their distinct chromosomal structures and sizes.

Traditionally, CRISPR tools have been tailored for mammalian cells and model species, resulting in weak and inconsistent efficiency when applied to microbes. Recognizing this limitation, Carrie Eckert, leader of the Synthetic Biology group at ORNL, remarked, “Few have been geared towards microbes where the chromosomal structures and sizes are very different.” This realization prompted the ORNL scientists to explore a new frontier in the quest to enhance the precision of CRISPR tools.

The team’s journey took an unconventional turn as they delved into quantum biology, a field at the intersection of molecular biology and quantum chemistry. Quantum biology explores the influence of electronic structure on the chemical properties and interactions of nucleotides, the fundamental building blocks of DNA and RNA, within cell nuclei where genetic material resides.

To improve the modeling and design of guide RNA for CRISPR Cas9, the scientists developed an explainable AI model named the iterative random forest. Trained on a dataset of approximately 50,000 guide RNAs targeting the genome of E. coli bacteria, the model took into account quantum chemical properties. The objective was to understand, at a fundamental level, the electronic distribution in nucleotides, which influences the reactivity and stability of the Cas9 enzyme-guide RNA complex.

“The model helped us identify clues about the molecular mechanisms that underpin the efficiency of our guide RNAs,” explained Erica Prates, a computational systems biologist at ORNL. The iterative random forest, with its thousands of features and iterative nature, was trained using the high-performance Summit supercomputer at ORNL’s Oak Ridge Leadership Computer Facility.

What sets this approach apart is its commitment to explainable AI. Rather than relying on a “black box” algorithm that lacks interpretability, the ORNL team aimed to understand the biological mechanisms driving results. Jaclyn Noshay, a former ORNL computational systems biologist and first author on the paper, emphasized, “We wanted to improve our understanding of guide design rules for optimal cutting efficiency with a microbial species focus.”

Graphical Abstract https://academic.oup.com/nar/article/51/19/10147/7279034

Validation of the explainable AI model involved CRISPR Cas9 cutting experiments on E. coli, using a large group of guides selected by the model. The results were promising, confirming the efficacy of the model in guiding genome modifications for microbes.

The implications of this research extend far beyond microbial genome editing. “If you’re looking at any sort of drug development, for instance, where you’re using CRISPR to target a specific region of the genome, you must have the most accurate model to predict those guides,” highlighted Carrie Eckert. The study not only advances the field of synthetic biology but also has broader applications in drug development and bioenergy research.

The ORNL researchers envision collaborative efforts with computational science colleagues to further enhance the microbial CRISPR Cas9 model using additional data from lab experiments and diverse microbial species. The ultimate goal is to refine CRISPR Cas9 models for a wide range of species, facilitating predictive DNA modifications with unprecedented precision.

The study, supported by the DOE Office of Science Biological and Environmental Research Program, ORNL’s Lab-Directed Research and Development program, and high-performance computing resources, signifies a significant leap forward in the quest to improve CRISPR technology. As Paul Abraham, a bioanalytical chemist at ORNL, remarked, “A major goal of our research is to improve the ability to predictively modify the DNA of more organisms using CRISPR tools. This study represents an exciting advancement toward understanding how we can avoid making costly ‘typos’ in an organism’s genetic code.” The findings hold promise for applications in fields ranging from bioenergy feedstock enhancement to drug development, marking a pivotal moment in the evolution of CRISPR technology.

Sources

https://doi.org/10.1093/nar/gkad736

traffic jam, automotive, row-688566.jpg

Bilateral Control: MIT’s answer to Traffic Jams

Automotive, Engineering, Mathematics / By

Navigating traffic can be a test of patience, especially when tailgating adds stress to an already congested commute. But what if a simple change in driving behavior could significantly ease traffic congestion and reduce travel time? New research from MIT suggests that maintaining a safe and equal distance between the car in front and the car behind could be a game-changer.

A computer simulation by MIT researchers showing traffic flow when equal distance on both the front and back is maintained (top) and when drivers focus on the vehicle in front (bottom)

Tailgating, aside from being aggressive and unsafe, exacerbates traffic jams, according to a study published in the journal IEEE Transactions on Intelligent Transportation Systems. The researchers propose a behavioral shift: drivers should consider not only the car in front but also the one behind, maintaining equilibrium to keep traffic flowing smoothly — in what they call “bilateral control”. This adjustment, backed by mathematical simulations, could potentially reduce commute times in half on certain roads.

The study’s co-author, Berthold Horn, a professor in MIT’s Department of Electrical Engineering and Computer Science expands on his previous work on “bilateral control” and takes a more macro level view in this new paper. He states “Birds have be doing this for centuries. To program this behavior, you’d want to look at the birds all around you and not just the ones in front of you.”

Evidently, he hopes that car companies incorporate rear sensors and update cruise control systems to account for these distances, so that traffic flow could significantly improve. However, the full benefits would only be realised if a substantial number of cars implement this system in the real world. According to Horn, traffic would improve drastically if just a small percentage of all cars implemented such systems. In future work funded in part by Toyota, he hopes to produce further simulations to test whether this method improves both the speed and safety of transportation on public road systems.

In conclusion, such systems can drastically improve transportation time and even reduce our global Carbon footprint by 25.4 billion kilograms of CO2.

https://ieeexplore.ieee.org/document/8861133
https://stormy.biology.utah.edu/publications/1984_Potts_Nature.pdf
https://people.csail.mit.edu/bkph/articles/Suppressing_Traffic_Flow%20Instabilities_IEEE_ITS_2013.pdf
https://math.mit.edu/traffic/

Microplastics are everywhere — but are they dangerous?

Ecology, Immunology, Medicine, Science / By

Originally perceived as a marine issue, with oceanographers estimating a total of 15–51 trillion microplastic particles floating on surface waters worldwide, scientists have recently discovered that these tiny particles can contaminate rivers, soils and air. Furthermore, these minuscule particles have been found in a range of food, human stool, and even made their way into some of Earth’s most remote regions; including the poles, the equator, and even Mount Everest.

Plastics are a group of materials, either synthetic or naturally occurring; used in numerous applications in our daily life. They are the third most abundant material, after concrete and steel, and are used in countless sectors; ranging from medicine to transport.

Microplastics are microscopic fragments of plastic debris, that usually emerge from plastic litter due to sunlight exposure, which causes the material to degrade and weaken over time; they can also come from plastic items due to wear and tear. For instance, up to 1.5 million microfibres, a type of microplastic, can be released per kilogram of clothing during a wash. Remarkably, even opening a plastic bottle can create thousands of microplastics. One may ask, are humans ingesting these minute particles?

The short answer is: yes, with the discovery of microplastics found in stool verifying this question. As of today, microplastics have been found in foods and drinks, mainly bottled and tap water, salt, dust, and more. According to a study conducted in Queensland, researchers studied samples of rice from different countries around the world, detecting microplastics in every sample; whether the rice was grown in Thailand, India, Pakistan, or Australia, and packaged in plastic or paper. In an interview, Dr Jake O’Brien, a lead author for Environmental Health Sciences, states “Washing the rice reduced the amount of plastic likely to be ingested. But the study used special filtered water for rinsing, and most households only have access to tap water; which contains microplastics.”

There currently isn’t enough evidence to say that microplastics are harmful, as the topic is relatively new. A lack of information and research surrounding the phenomenon is scarce, as scientists aim to establish an evidence base. Prof Ian Musgrave, a toxicologist at the University of Adelaide, expresses “Knowing if microplastics are harmful to humans is hard to untangle when we are exposed to so many other substances. While we are consuming things that have tiny amounts of microplastics, we don’t absorb them. But because we can’t demonstrate damage, that’s not a reason to be casual.” Additionally, this explains why multiple studies on the ingestion of microplastics by marine animals, can’t completely isolate the impact microplastics have against all the other pollution and pressure they are exposed to in the environment, as it’s difficult to perform.

Likewise, there are emerging studies on the effects of ingesting high levels of microplastics in rats and mice, concluding that high levels of microplastic accumulation can affect reproduction. Nevertheless, it is more likely that the smaller the particles the greater the potential to cause harm, as smaller specks have an easier chance of entering cells or tissues; however, quantifying these issues and understanding where they come from is a challenge.

While the debate is still ongoing as to whether microplastic could cause harm, you may still wish to limit your exposure. To limit your exposure, you can drink filtered tap water, and choose natural-based products over plastic for yourself and your environment will help reduce microplastic exposure. Overall, minimising microplastic exposure globally requires a substantial effort to limit the release of plastics, and microplastics, to the environment. Reducing plastic waste, washing your clothes less often, and bringing your own bag whilst shopping; all can contribute to limiting plastic release and even production; thus decreasing microplastic exposure.

Whatever the solution, it’s important that it’s better for both the planet and people.

Lab-grown meat: Incredible or Inedible?

Bio Chemistry, Biology, Biotech, Science, Technology / By

Scientists are currently cultivating proteins from the stem cells of livestock and poultry in labs in a bid to create more sustainable meat, but will anyone want to eat it?

Lab-grown meat, although a promising concept, has been slow to hit the mainstream. The notion is to grow meat, within laboratory conditions, by extracting stem cells from live animals and installing them into a bioreactor (vessel-like device), where salts, vitamins, sugars, and proteins are added. The oxygen-rich temperature-controlled environment allows the stem cells to multiply dramatically; eventually differentiating into muscle fibres that cluster together, aided by scaffolding material.

Numerous start-ups and companies have invested millions into this innovative technology. Eat Just, valued at $1.2 billion, was founded by Josh Tetrick in 2011, and the company began the development of lab-grown chicken in 2016. “With the aid of a 1,200-liter bioreactor, the cells can develop into meat at a rapid rate with the whole process taking around 14 days. For comparison, the production of farm-based chicken is a 45-day process”, states the CEO of Eat Just. Evidently, lab-grown meat rivals the production of farm-based alternatives; by providing a more efficient development procedure.

Currently, the meat industry slaughters tens of billions of animals every year, and meat consumption is expected to increase by more than 70% by the year 2050; according to the Food and Agriculture Organisation of the United Nations. At the current state, lab-grown meat products will struggle to satisfy these demands. To put this into perspective, to produce enough meat to feed everyone in Singapore, Eat Just would need to use 10,000-litre bioreactors, over more this process is currently more expensive than traditional farming methods. However, with increased funding, it might soon become a reality.

Despite these challenges, the advancement of lab-grown meat products will continue, promising a wealth of benefits. Lab-grown meat is drug-free, cruelty-free, more environmentally friendly, and sustainable. One report estimates that lab-produced meats could lower greenhouse emissions by 78–96%, 99% less land use, and 82–96% less water consumption. It is, without a doubt, more sustainable than traditional meat farming.

In spite of all adversities, at the end of last year, restaurant 1880 in Singapore became the first in the world to serve lab-grown meat, after approval from the country’s food agency on the sale of cultured meat. This poses as a huge stepping stone for the future of lab-grown meat. One estimate by US consultancy firm Kearney suggests that 35 per cent of all meat consumed globally will be cell-based by 2040.

In an earlier interview, Josh Tetrick (founder of EatJust) expresses, “Working in partnership with the broader agriculture sector and forward-thinking policymakers, companies like ours can help meet the increased demand for animal protein as our population climbs to 9.7 billion by 2050.”

It is beyond dispute that the status quo is not sustainable. So, do we have the appetite for change?