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AI plus gene editing promises to shift biotech into high gear

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theconversation.com – Marc Zimmer, Professor of Chemistry, Connecticut College – 2024-06-06 07:47:02

AI plus gene editing promises to shift biotech into high gear

AI knowledge combined with gene-editing precision the way to dial-a-protein.
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Marc Zimmer, Connecticut College

During her chemistry Nobel Prize lecture in 2018, Frances Arnold said, “Today we can for all practical purposes read, write and edit any sequence of DNA, but we cannot compose it.” That isn't true anymore.

Since then, science and technology have progressed so much that artificial intelligence has learned to compose DNA, and with genetically modified bacteria, scientists are on their way to designing and making bespoke proteins.

The goal is that with AI's designing talents and gene editing's engineering abilities, scientists can modify bacteria to act as mini factories producing new proteins that can reduce greenhouse gases, digest plastics or act as species-specific pesticides.

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As a chemistry professor and computational chemist who studies molecular science and environmental chemistry, I believe that advances in AI and gene editing make this a realistic possibility.

Gene sequencing – reading life's recipes

All living things contain genetic materials – DNA and RNA – that the hereditary information needed to replicate themselves and make proteins. Proteins constitute 75% of human dry weight. They make up muscles, enzymes, hormones, blood, hair and cartilage. Understanding proteins means understanding much of biology. The order of nucleotide bases in DNA, or RNA in some viruses, encodes this information, and genomic sequencing technologies identify the order of these bases.

The Human Genome Project was an international effort that sequenced the entire human genome from 1990 to 2003. Thanks to rapidly improving technologies, it took seven years to sequence the first 1% of the genome and another seven years for the remaining 99%. By 2003, scientists had the complete sequence of the 3 nucleotide base pairs coding for 20,000 to 25,000 genes in the human genome.

However, understanding the functions of most proteins and correcting their malfunctions remained a .

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AI learns proteins

Each protein's shape is critical to its function and is determined by the sequence of its amino acids, which is in turn determined by the gene's nucleotide sequence. Misfolded proteins have the wrong shape and can cause illnesses such as neurodegenerative diseases, cystic fibrosis and Type 2 diabetes. Understanding these diseases and developing treatments requires knowledge of protein shapes.

Before 2016, the only way to determine the shape of a protein was through X-ray crystallography, a laboratory technique that uses the diffraction of X-rays by single crystals to determine the precise arrangement of atoms and molecules in three dimensions in a molecule. At that time, the structure of about 200,000 proteins had been determined by crystallography, costing billions of dollars.

AlphaFold, a machine learning program, used these crystal structures as a set to determine the shape of the proteins from their nucleotide sequences. And in less than a year, the program calculated the protein structures of all 214 million genes that have been sequenced and published. The protein structures AlphaFold determined have all been released in a freely available database.

To effectively address noninfectious diseases and design new , scientists need more detailed knowledge of how proteins, especially enzymes, bind small molecules. Enzymes are protein catalysts that enable and regulate biochemical reactions.

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AI system AlphaFold3 allows scientists to make intricately detailed models of life's molecular machinery.

AlphaFold3, released May 8, 2024, can predict protein shapes and the locations where small molecules can bind to these proteins. In rational drug design, drugs are designed to bind proteins involved in a pathway related to the disease being treated. The small molecule drugs bind to the protein binding site and modulate its activity, thereby influencing the disease path. By being able to predict protein binding sites, AlphaFold3 will enhance researchers' drug capabilities.

AI + CRISPR = composing new proteins

Around 2015, the development of CRISPR technology revolutionized gene editing. CRISPR can be used to find a specific part of a gene, change or delete it, make the cell express more or less of its gene product, or even add an utterly foreign gene in its place.

In 2020, Jennifer Doudna and Emmanuelle Charpentier received the Nobel Prize in chemistry “for the development of a method (CRISPR) for genome editing.” With CRISPR, gene editing, which once took years and was species specific, costly and laborious, can now be done in days and for a fraction of the cost.

AI and genetic engineering are advancing rapidly. What was once complicated and expensive is now routine. Looking ahead, the dream is of bespoke proteins designed and produced by a combination of machine learning and CRISPR-modified bacteria. AI would design the proteins, and bacteria altered using CRISPR would produce the proteins. Enzymes produced this way could potentially breathe in carbon dioxide and methane while exhaling organic feedstocks, or break down plastics into substitutes for concrete.

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I believe that these ambitions are not unrealistic, given that genetically modified organisms already account for 2% of the U.S. economy in agriculture and pharmaceuticals.

Two groups have made functioning enzymes from scratch that were designed by differing AI . David Baker's Institute for Protein Design at the of Washington devised a new deep-learning-based protein design strategy it named “family-wide hallucination,” which they used to make a unique light-emitting enzyme. Meanwhile, biotech startup Profluent, has used an AI trained from the sum of all CRISPR-Cas knowledge to design new functioning genome editors.

If AI can learn to make new CRISPR systems as well as bioluminescent enzymes that work and have never been seen on Earth, there is hope that pairing CRISPR with AI can be used to design other new bespoke enzymes. Although the CRISPR-AI combination is still in its infancy, once it matures it is likely to be highly beneficial and could even the world tackle climate change.

It's important to remember, however, that the more powerful a technology is, the greater the risks it poses. Also, humans have not been very successful at engineering nature due to the complexity and interconnectedness of natural systems, which often leads to unintended consequences.The Conversation

Marc Zimmer, Professor of Chemistry, Connecticut College

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This article is republished from The Conversation under a Creative Commons license. Read the original article.

The Conversation

Supreme Court kicks cases about tech companies’ First Amendment rights back to lower courts − but appears poised to block states from hampering online content moderation

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theconversation.com – Lynn Greenky, Professor Emeritus of Communication and Rhetorical Studies, Syracuse – 2024-07-01 15:26:42
How much power do social companies have over what users post?
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Lynn Greenky, Syracuse University

The has sent back to lower courts the about whether states can block social media companies such as Facebook and X, formerly Twitter, from regulating and controlling what users can post on their platforms.

Laws in Florida and Texas sought to impose restrictions on the internal policies and algorithms of social media platforms in ways that influence which posts will be promoted and spread widely and which will be made less visible or even .

In the unanimous decision, issued on July 1, 2024, the high court remanded the two cases, Moody v. NetChoice and NetChoice v. Paxton, to the 11th and 5th U.S. Circuit Courts of Appeals, respectively. The court admonished the lower courts for their failure to consider the full force of the laws' applications. It also warned the lower courts to consider the boundaries imposed by the Constitution against government interference with private speech.

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Contrasting views of social media sites

In their arguments before the court in February 2024, the two sides described competing visions of how social media fits into the often overwhelming flood of information that defines modern digital society.

The states said the platforms were mere conduits of communication, or “speech hosts,” similar to legacy telephone companies that were required to carry all calls and prohibited from discriminating against users. The states said that the platforms should have to carry all posts from users without discrimination among them based on what they were saying.

The states argued that the content moderation rules the social media companies imposed were not examples of the platforms themselves speaking – or choosing not to speak. Rather, the states said, the rules affected the platforms' behavior and caused them to censor certain views by allowing them to determine whom to allow to speak on which topics, which is outside First Amendment protections.

By contrast, the social media platforms, represented by NetChoice, a tech industry trade group, argued that the platforms' guidelines about what is acceptable on their sites are protected by the First Amendment's guarantee of speech free from government interference. The companies say their platforms are not public forums that may be subject to government regulation but rather private services that can exercise their own editorial judgment about what does or does not appear on their sites.

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They argued that their policies were aspects of their own speech and that they should be allowed to develop and implement guidelines about what is acceptable speech on their platforms based on their own First Amendment rights.

Here's what the First Amendment says and what it means.

A reframe by the Supreme Court

All the litigants – NetChoice, and Florida – framed the issue around the effect of the laws on the content moderation policies of the platforms, specifically whether the platforms were engaged in protected speech. The 11th U.S. Circuit Court of Appeals upheld a lower court preliminary injunction against the Florida law, holding the content moderation policies of the platforms were speech and the law was unconstitutional.

The 5th U.S. Circuit Court of Appeals came to the opposite conclusion and held that the platforms were not engaged in speech, but rather the platform's algorithms controlled platform behavior unprotected by the First Amendment. The 5th Circuit determined the behavior was censorship and reversed a lower court injunction against the Texas law.

The Supreme Court, however, reframed the inquiry. The court noted that the lower courts failed to consider the full range of activities the laws covered. Thus, while a First Amendment inquiry was in order, the decisions of the lower courts and the arguments by the parties were incomplete. The court added that neither the parties nor the lower courts engaged in a thorough analysis of whether and how the states' laws affected other elements of the platforms' products, such as Facebook's direct messaging applications, or even whether the laws have any impact on email providers or online marketplaces.

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The Supreme Court directed the lower courts to engage in a much more exacting analysis of the laws and their implications and provided some guidelines.

First Amendment principles

The court held that content moderation policies reflect the constitutionally protected editorial choices of the platforms, at least regarding what the court describes as “heartland applications” of the laws – such as Facebook's News Feed and YouTube's homepage.

The Supreme Court required the lower courts to consider two core constitutional principles of the First Amendment. One is that the amendment protects speakers from being compelled to communicate messages they would prefer to exclude. Editorial discretion by entities, including social media companies, that compile and curate the speech of others is a protected First Amendment activity.

The other principle that the amendment precludes the government from controlling private speech, even for the purpose of balancing the marketplace of ideas. Neither nor federal government may manipulate that marketplace for the purposes of presenting a more balanced array of viewpoints.

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The court also affirmed that these principles apply to digital media in the same way they apply to traditional or legacy media.

In the 96-page opinion, Justice Elena Kagan wrote: “The First Amendment … does not go on when social media are involved.” For now, it appears the social media platforms will continue to control their content.The Conversation

Lynn Greenky, Professor Emeritus of Communication and Rhetorical Studies, Syracuse University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Disability community has long wrestled with ‘helpful’ technologies – lessons for everyone in dealing with AI

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theconversation.com – Elaine Short, Assistant Professor of Computer Science, Tufts – 2024-07-01 07:19:34

A robotic arm helps a disabled person paint a picture.

Jenna Schad /Tufts University

Elaine Short, Tufts University

You might have heard that artificial intelligence is going to revolutionize everything, save the world and give everyone superhuman powers. Alternatively, you might have heard that it will take your job, make you lazy and stupid, and make the world a cyberpunk dystopia.

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Consider another way to look at AI: as an assistive technology – something that helps you function.

With that view, also consider a community of experts in giving and receiving assistance: the disability community. Many disabled people use technology extensively, both dedicated assistive technologies such as wheelchairs and general-use technologies such as smart home devices.

Equally, many disabled people professional and casual assistance from other people. And, despite stereotypes to the contrary, many disabled people regularly give assistance to the disabled and nondisabled people around them.

Disabled people are well experienced in receiving and giving social and technical assistance, which makes them a valuable source of insight into how everyone might relate to AI systems in the future. This potential is a key driver for my work as a disabled person and researcher in AI and robotics.

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Actively learning to live with help

While virtually everyone values independence, no one is fully independent. Each of us depends on others to grow our food, care for us when we are ill, give us advice and emotional , and us in thousands of interconnected ways. Being disabled means support needs that are outside what is typical and therefore those needs are much more visible. Because of this, the disability community has reckoned more explicitly with what it means to need help to than most nondisabled people.

This disability community perspective can be invaluable in approaching new technologies that can assist both disabled and nondisabled people. You can't substitute pretending to be disabled for the experience of actually being disabled, but accessibility can benefit everyone.

The curb-cut effect – how technologies built for disabled people help everyone – has become a principle of good design.

This is sometimes called the curb-cut effect after the ways that putting a ramp in a curb to help a wheelchair user access the sidewalk also people with strollers, rolling suitcases and bicycles.

Partnering in assistance

You have probably had the experience of someone to help you without listening to what you actually need. For example, a parent or friend might “help” you clean and instead end up hiding everything you need.

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Disability advocates have long battled this type of well-meaning but intrusive assistance – for example, by putting spikes on wheelchair handles to keep people from pushing a person in a wheelchair without being asked to or advocating for services that keep the disabled person in control.

The disabled community instead offers a model of assistance as a collaborative effort. Applying this to AI can help to ensure that new AI tools support human autonomy rather than taking over.

A key goal of my lab's work is to develop AI-powered assistive robotics that treat the user as an equal partner. We have shown that this model is not just valuable, but inevitable. For example, most people find it difficult to use a joystick to move a robot arm: The joystick can only move from front to back and side to side, but the arm can move in almost as many ways as a human arm.

The author discusses her work on robots that are designed to help people.

To help, AI can predict what someone is planning to do with the robot and then move the robot accordingly. Previous research assumed that people would ignore this help, but we found that people quickly figured out that the system is doing something, actively worked to understand what it was doing and tried to work with the system to get it to do what they wanted.

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Most AI systems don't make this easy, but my lab's new approaches to AI empower people to influence robot behavior. We have shown that this results in better interactions in tasks that are creative, like painting. We also have begun to investigate how people can use this control to solve problems outside the ones the robots were designed for. For example, people can use a robot that is trained to carry a cup of to instead pour the water out to water their plants.

Training AI on human variability

The disability-centered perspective also raises concerns about the huge datasets that power AI. The very nature of data-driven AI is to look for common patterns. In general, the better-represented something is in the data, the better the model works.

If disability means having a body or mind outside what is typical, then disability means not being well-represented in the data. Whether it's AI systems designed to detect cheating on exams instead detecting students' disabilities or robots that fail to account for wheelchair users, disabled people's interactions with AI reveal how those systems are brittle.

One of my goals as an AI researcher is to make AI more responsive and adaptable to real human variation, especially in AI systems that learn directly from interacting with people. We have developed frameworks for testing how robust those AI systems are to real human teaching and explored how robots can learn better from human teachers even when those teachers change over time.

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Thinking of AI as an assistive technology, and learning from the disability community, can help to ensure that the AI systems of the future serve people's needs – with people in the driver's seat.The Conversation

Elaine Short, Assistant Professor of Computer Science, Tufts University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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How was popcorn discovered? An archaeologist on its likely appeal for people in the Americas millennia ago

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theconversation.com – Sean Rafferty, Professor of Anthropology, University at Albany, State University of New York – 2024-07-01 07:19:19

Could a spill by the cook fire have been popcorn's eureka moment?

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Sean Rafferty, University at Albany, State University of New York

Curious Kids is a for of all ages. If you have a question you'd like an expert to answer, send it to curiouskidsus@theconversation.com.

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How was popcorn discovered? – Kendra, age 11, Penn Yan, New York


You have to wonder how people originally figured out how to eat some foods that are beloved . The cassava plant is toxic if not carefully processed through multiple steps. Yogurt is basically old milk that's been around for a while and contaminated with bacteria. And who discovered that popcorn could be a toasty, tasty treat?

These kinds of food mysteries are pretty hard to solve. Archaeology depends on solid remains to figure out what happened in the past, especially for people who didn't use any sort of writing. Unfortunately, most stuff people traditionally used made from wood, animal materials or cloth decays pretty quickly, and archaeologists like me never find it.

We have lots of evidence of hard stuff, such as pottery and stone tools, but softer things – such as leftovers from a meal – are much harder to find. Sometimes we get lucky, if softer stuff is found in very dry places that preserve it. Also, if stuff gets burned, it can last a very long time.

Corn's ancestors

Luckily, corn – also called maize – has some hard parts, such as the kernel shell. They're the bits at the bottom of the popcorn bowl that get caught in your teeth. And since you have to heat maize to make it edible, sometimes it got burned, and archaeologists find evidence that way. Most interesting of all, some plants, maize, contain tiny, rock-like fragments called phytoliths that can last for thousands of years.

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green plant stalks with reddish tendrils

The ancestor of maize was a grass called teosinte.

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Scientists are pretty sure they know how old maize is. We know maize was probably first farmed by Native Americans in what is now Mexico. Early farmers there domesticated maize from a kind of grass called teosinte.

Before farming, people would gather wild teosinte and eat the seeds, which contained a lot of starch, a carbohydrate like you'd find in bread or pasta. They would pick teosinte with the largest seeds and eventually started weeding and planting it. Over time, the wild plant developed into something like what we call maize today. You can tell maize from teosinte by its larger kernels.

There's evidence of maize farming from dry caves in Mexico as early as 9,000 years ago. From there, maize farming spread throughout North and South America.

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Popped corn, preserved food

Figuring out when people started making popcorn is harder. There are several types of maize, most of which will pop if heated, but one variety, actually called “popcorn,” makes the best popcorn. Scientists have discovered phytoliths from Peru, as well as burned kernels, of this type of “poppable” maize from as early as 6,700 years ago.

cobs of popcorn over popped kernels, one showing popping on the cob

Each popcorn kernel is a seed, ready to burst when heated.

Rick Madonik/Toronto Star via Getty Images

You can imagine that popping maize kernels was first discovered by . Some maize probably fell into a cooking fire, and whoever was nearby figured out that this was a handy new way of preparing the food. Popped maize would last a long time and was easy to make.

Ancient popcorn was probably not much like the snack you might munch at the theater today. There was probably no salt and definitely no butter, since there were no cows to milk in the Americas yet. It probably wasn't served hot and was likely pretty chewy compared with the version you're used to today.

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It's impossible to know exactly why or how popcorn was invented, but I would guess it was a clever way to preserve the edible starch in corn by getting rid of the little bit of inside each kernel that would make it more susceptible to spoiling. It's the heated water in the kernel escaping as steam that makes popcorn pop. The popped corn could then last a long time. What you may consider a tasty snack today probably started as a useful way of preserving and storing food.


Hello, curious kids! Do you have a question you'd like an expert to answer? Ask an adult to send your question to CuriousKidsUS@theconversation.com. Please tell us your name, age and the where you .

And since curiosity has no age limit – adults, let us know what you're wondering, too. We won't be able to answer every question, but we will do our best.The Conversation

Sean Rafferty, Professor of Anthropology, University at Albany, State University of New York

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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