The human genome has long been a difficult book to read. Modern technological advances have recently opened doors for researchers to begin asking a big question: What parts of our DNA sequences might influence disease? Mary Lauren Benton, Ph.D., recently joined the Baylor Engineering and Computer Science faculty as an assistant professor of bioinformatics, and she is working to answer that question.

Mary Lauren Benton, Ph.D.

If you think of the genome like an instruction manual, Im interested in the grammar, Benton said. Im interested in understanding how short DNA sequences turn genes on and off in different cells and allow for many different outcomes. If we know how a particular sequence influences risk of heart disease, for example, we can use that information to help us guide clinical decisions, whether thats applying different treatments, prescribing different medications or scheduling more preventative care. All of these things can help clinicians to better prioritize and care for patients.

Benton uses computer modeling to look through large data sets of genetic information. Bioinformatics allows for processing of these large data in ways not possible previously, giving room for biological researchers to find patterns and solutions using methods and tools from computer science.

I think of bioinformatics as the intersection of computer science and biology, Benton said. I take tools and methods from computer science, and I apply them to solve fundamental biological questions. We have a lot of really big data sets in biology. The human genome is 3 billion base pairs long, which we cant analyze by hand. The tools from computer science and statistics give us a way to ask questions that we wouldnt be able to otherwise. They open the doors to analyses that would have been impossible even 10 or 20 years ago.

Benton most recently authored The Influence of Evolutionary History on Human Health and Disease, which was published in the Nature Reviews Genetic Journal and takes a look at the evolutionary origins of disease. Being diagnosed with a disease or health problem may feel like a present problem; however, Benton explained that looking at the foundations of a disease is important to understanding how to move forward with treatment.

The foundations and the systems that are involved in disease have really deep evolutionary origins, she said. Cancer might be something that youre diagnosed with today, but the foundation of cancer can be traced back to the idea that we have cells that are able to grow and divide, which also provides the opportunity for tumors to grow.

Benton explained that its important to consider the history of the disease and the systems involved alongside any variants or environmental factors that help to cause the disease. A holistic understanding of disease can influence how patients are treated as well as provide information about how their diseases came to be.

Its not enough to understand whats happening in a person right now or in the last five years, Benton said. Understanding the million-year history of how people got here is equally important to make advances in personalizing medicine, especially genomic medicine. Having that long lens is something that is often lost in the day-to-day operations of a doctors office.

Benton is excited to be evaluating the way that researchers think about decoding genetic information. While a common approach is to think of genes as being able to be turned off or on with a simple switch, that may not be the most accurate approach.

We study these sets of genetic switches and how they turn genes on and off at the right times. Often, we think about these switches working one-at-a-time; the gene is either on or its off, Benton said. But it is much more complicated than that. There are often multiple switches that act more like a dashboard of knobs and dials that all work together to properly tune the output of the genome.

Bentons research is moving toward the development of new models and ways of thinking about how known individual elements are combined and factored into this much larger, more accurate dashboard. Differences based on demographic histories, environmental variables and evolutionary processes all influence the risk of disease in different ways. A better understanding of genomes and how genetic variants relate to disease has major implications for precision medicine.

Its really vital for precision medicine to take into account the full diversity of the human experience. We cant focus on one particular kind of person or one population. People of European ancestry are over-represented in genetic studies, Benton said. Improving diversity and representation in our genomic studies is vital to understanding how the genome relates to disease and to learning how to appropriately treat all of the patients that might walk through the doors of a clinic.

Precision medicine, in some ways, seems futuristic and far-off. But, in other ways, precision medicine is already being used to protect at-risk individuals from diseases like cancer. While widespread precision medicine may not be seen for a long time, research like Bentons plays a role in better understanding disease risk broadly and providing context for clinical solutions moving forward.

Precision medicine is both happening right now and is something that well probably always be working toward, Benton said. There are things that we understand right now about specific genetic variants that might predispose you to a certain kind of breast cancer, for example. We already have diseases that we can test for or treat differently based on someones genotype. But, because the genome is such a complicated thing, walking into the clinic and handing your DNA sequence to the doctor, who would then read it and prescribe the right treatments on the spot, is a goal that well always be working toward. Still, I expect well see big changes in the next five to 10 years given the current rate of progress.

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Grammar of the Genome: Reading the Influence of DNA on Disease - Baylor University

The relentless ping-pong of our email inbox is a workplace distraction that can lead to lost focus and a daily to-do list that doesn't get done.

Over several years, Georgetown University Professor Cal Newport has whittled down his email checks to just once or twice a week.

Newport is perhaps best known for his 2016 book "Deep Work", about how to overcome distraction to focus. His latest book, "A World Without Email", explores how people can cut the noise surrounding their inboxes.

His theory is that it is the "hyperactive hive mind" and the associated back-and-forth messaging between colleagues to make decisions stops us from focussing, denting our productivity and sense of calm.

"There are two ways to attack the problem," he tells Insider. "One is to tackle your habits and how you interact with your inbox.

"It assumes the communication is necessary and questions how often you check it and how you write the messages you have to send."

"The second is the way you work and collaborate: the workflows, rules and guidelines. You need to get specific and intentional about those underlying processes, spelling out how you want to communicate."

These are his four tips on how to limit the impact of the email tsunami on your work.

1. Reduce unscheduled emails

The main issue isn't inbox-checking while you work but the attention-hungry "unscheduled" messages that filter into them, Newport says.

You are doing something, then an unexpected email lands, distracting you and possibly prompting a stream of replies.

"Businesses should ask is 'How do we minimize how many emails will arrive at an unscheduled time and in turn will require a response?'"

This entails finding better processes for communicating be it on the phone or via a project organization board such as Trello to allow you to maintain focus.

"Put in place another method of collaborating that gets the job done, with less messaging," Newport says, adding that if you just check inboxes less often, you will simply respond to things more slowly.

For the recent launch of his book, Newport and his publicity team decided to create a shared document.

They would enter interview opportunities, he would add notes, confirm dates and accept calendar invites. In emergencies, his team could call or text.

"Roughly 200 inbox checks were replaced with a couple of checks a week," Newport says. "For me, that's a huge win. You don't want to prioritize in-the-moment convenience, you want to prioritize eliminating unscheduled messages that require context shifts."

Setting rules and guidelines is also crucial for dealing with clients a clear communication system from day one will ensure customer confidence as well as your ability to deep-work, says Newport.

"Clarity trumps accessibility," he adds.

2. If your workplace won't change, change yourself but don't feel like you have to announce it

Until companies decide otherwise, it's likely most will continue to rely on rapid email checks and responses to make decisions. So, Newport said, you should lead the way.

To kick-start personal change, Newport recommends identifying the key tasks of your working day and from there, ascertaining what duty requires what kind of communication for optimal performance.

But announcing your new email attitude to all and sundry isn't necessary. "Don't advertise the changes you're making and why that just gives hard edges for people to push up against," he said.

"You could even be nudging your team towards these new processes without them knowing it."

3. Limit the ways you can access your inbox

If your reflexive instinct is to check your email on your phone, remove the temptation.

Having identified his phone's inbox as a focus drain ("I was very frustrated with it for a long time") and realizing he was looking at it "as something to do", Newport uninstalled his emails and chose not to authenticate Google on the device, meaning he couldn't check that way either.

Instead, he now looks at his inbox "once or twice" a week, intentionally logging on to a computer rather than idly opening an app.

Another trick, counterintuitively, is to have multiple email addresses. Newport currently has six different addresses, each for different communication strands.

This means he can check the most relevant account, without the noise of the others, doing away with the "inefficiency" of an allpurpose inbox.

4. Think about the post-WFH workplace Newport is expanding his face-to-face office hours to make up for his email reduction

A year of remote working has intensified messaging. Some of this may die down when offices reopen.

"It's social psychology," Newport adds. "If I see you in person, I'm likely to think twice about emailing you something that will put more work on your plate."

But as workplaces prepare to reopen post-lockdown, there is a great opportunity to consider what you want for the future of your communications.

Newport already has a plan for when he returns to campus in the fall.

"I'm going to lean into office hours harder when we're back on campus," he says. "I'm probably going to make them longer, so I can handle more.

"I have a lot of students, including those who want to talk about my books or my podcast, and I always just say: 'here's my office hours, my door's open'. I want to push back more towards that."

He adds: "Until we can get rid of the underlying assumption that back-and-forth messages is how to figure things out, we're not going to solve the problem.

"The focus needs to move from 'individuals are approaching their inboxes wrong' to 'organizations are organizing their work wrong'."

Link:

How to Cut Back on Emails, From the Professor Who Checks His Inbox 'Once or Twice' a Week - Business Insider

At first, science writer John Horgan (pictured), author of a number of books including The End of Science (1996), accepted the conventional AI story:

When I started writing about science decades ago, artificial intelligence seemed ascendant. IEEE Spectrum, the technology magazine for which I worked, produced a special issue on how AI would transform the world. I edited an article in which computer scientist Frederick Hayes-Roth predicted that AI would soon replace experts in law, medicine, finance and other professions.

But that year, 1984, ushered in an AI winter, in which innovation stalled and funding dried up. By 1998, problems like non-recurrent engineering had begun to be recognized: Algorithms that can perform a specialized task, like playing chess, cannot be easily adapted for other purposes.

Today, while AI appears to be booming, Horgan says, hype frustrates critical appraisal of advances. For example, many readers may be surprised to learn this item from his recent Scientific American article:

Google Healths claim in Nature that its AI program had outperformed professionals in diagnosing breast cancer is suspect: In October, a group led by Benjamin Haibe-Kains, a computational genomics researcher, criticized the Google health paper, arguing that the lack of details of the methods and algorithm code undermines its scientific value. The problem is, the details are in the code and Google wont share the code. An article on that question from MITs Technology Review tells us, AI is wrestling with a replication crisis: Tech giants dominate research but the line between real breakthrough and product showcase can be fuzzy.

If you hadnt heard that, you are not alone. We dont hear much about failures, stalls, and dubious claims around AI because, generally speaking, media follow a special standard when covering it: Progress is simply assumed. Outrageous hype is forgivable. Astounding claims are not queried. Stalls and failures are minimized rather than highlighted. And the possibility that some prophesied advances may be impossible in practice because the problems are not computable is seldom entertained possibly not even understood.

Perhaps the most interesting thing Horgan learned from Larson before The Myth of Artificial Intelligence was published is that there is a very large mystery at the heart of intelligence, which no one currently has a clue how to solve:

Put bluntly: all evidence suggests that human and machine intelligence are radically different. And yet the myth of inevitability persists.

When I first started writing about science, I believed the myth of AI. One day, surely, researchers would achieve the goal of a flexible, supersmart, all-purpose artificial intelligence, like HAL. Given rapid advances in computer hardware and software, it was only a matter of time. And who was I to doubt authorities like Marvin Minsky?

In 1998, computer pioneer Marvin Minsky (19272016, pictured) told an interviewer,

My goal is making machines that can thinkby understanding how people think. One reason why we find this hard to do is because our old ideas about psychology are mostly wrong. Most words we use to describe our minds (like consciousness, learning, or memory) are suitcase-like jumbles of different ideas. Those old ideas were formed long ago, before computer science appeared. It was not until the 1950s that we began to develop better ways to help think about complex processes.

In 1995 philosopher David Chalmers coined the term Hard Problem of consciousness as a way of categorizing a problem that is not a big suitcase and defies so simple a solution as computer science.

Horgan meanwhile became, as he puts it, an AI doubter. Of Larsons Myth, he says, Erik Larson exposes the vast gap between the actual science underlying AI and the dramatic claims being made for it. In his Scientific American piece, he reflects, our mindsin spite of enormous advances in neuroscience, genetics, cognitive science and, yes, artificial intelligenceremain as mysterious as ever.

Actual mysteries may be fruitful if we can live with them; false solutions are not.

Note 1: Most recently, Horgan has published a book, MindBody Problems, which is free to read at his site.

Note 2: The photo of Marvin Minsky is courtesy Sethwoodworth at English Wikipedia. Transferred from en.wikipedia to Commons by Mardetanha using CommonsHelper., CC BY 3.0

You may also wish to read design theorist William Dembskis takes on Larsons Myth:

New book massively debunks our AI overlords: Aint gonna happen AI researcher and tech entrepreneur Eric J. Larson expertly dissects the AI doomsday scenarios. Many thinkers have tried to stem the tide of hype but, as an information theorist points out, no one has done it so well.

and

No AI overlords?: What is Larson arguing and why does it matter? Information theorist William Dembski explains, computers cant do some things by their very nature.

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Why Did a Prominent Science Writer Come To Doubt the AI Takeover? - Walter Bradley Center for Natural and Artificial Intelligence

Special to The Alliance Review

BELOIT West Branch Local Schools has invited the community to its STEM night from 6 to 8 p.m. Monday.

Doors open at 6 p.m., when students will display projects and engage with members of the public in conversation about their projects and classes. A program presentation will begin at 7 p.m., with recognition of community organizations and businesses that have sponsored the program.

The event will be in the Old Gym, at 14277 S. Main St. in Beloit. Visitors should park in the south lot.

Student displays will highlight projects from science, technology, engineering and mathematics (which make up STEM). Classes include engineering, biomedical science, computer science, design and modeling, coding, computer applicationsand medical detectives.

The community has been so supportive of the STEM program here at West Branch, says Evelyn Woods, assistant principal of West Branch High School and STEM coordinator. We are excited for students to share what theyre learning with the community and to recognize our generous supporters that have made these classes possible.

Sponsors that will be recognized for their support of the STEM programs for the 2020-2021 school year includeAultman Alliance Community Hospital;BOC Water Hydraulics;Butech Bliss;CTM Labeling System;Damascus PIE;FedEx;MAC Trailer;Morgan Engineering;Middle School PIE;Salem Community Hospital;SES;Simmers Crane;Sebring West Branch Foundation; and an anonymous donor.

Some sponsors have already extended their support with a commitment to sponsor these growing programs for the 2021-22 school year, including Aultman Alliance Community Hospital, Butech Bliss, CTM Labeling System, Simmers Crane,and an anonymous donor.

We are grateful for the continued support of our community in growing these programs, says Woods. The skills and knowledge our students gain from these classes will set a strong foundation for their future.

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Public invited to West Branch STEM showcase - The-review