Curating the Internet: Science and technology micro-summaries for September 28, 2019

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Authored by @remlaps

Provable and tractable algorithms for protein design; A researcher theorizes that obesity is growing because of "ultra-processed" foods; Message rate limiting reduces the spread of misinformation on whatsapp; How to fix unbootable Macs after Google Chrome corrupted them; and post-secondary cybersecurity curriculum guidelines

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  1. Protein Design by Provable Algorithms - Focusing on design techniques that start with an existing protein and make step-wise alterations to design new ones, Mark A. Hallen and Bruce R. Donald offer the following key points. Protein design algorithms that can be used for new therapeutics are able to optimize proteins for characteristics like strength and stability. And these algorithms include highly efficient, provably correct methods, where recent advances have introduced more realistic models of protein chemistry. Continuing on, the article describes techniques for continuously flexible protein design that arose because the continuous search-space of possible protein sequences is too large for an exhaustive search. As a result, researchers made use of optimization techniques that were built upon a discrete optimization problem in order to develop mixed discrete-continuous optimization techniques that are tractable and can optimize for one or more desirable protein characteristics. They report that the technique also holds promise for improvement under GPU execution and parallel processing. Thus far, the techniques have been used to transform one input molecule to another, predicted enzyme resistance to particular antibiotics, and shown promise for the design of therapeutics. The algorithms also have potential to help drug development for non-protein drugs, because they enable sub-linear search for a large space of drug candidates.

    Here is a video:

  2. A New Theory of Obesity - Fats, carbohydrates, and sugars are commonly blamed for the obesity epidemic, but Kevin Hall, from the NIH, disagrees. His research suggests that obesity is becoming more common because of the prevalence of "ultra-processed foods", foods that are made by tearing ingredients apart and then reconstituting them in forms like frosted cakes or ready-to-eat meals. His research, which avoided the reliance on self-reporting by using volunteers who were hospitalized, suggests that when people are encouraged to eat freely and given the choice between processed and unprocessed foods, they'll eat more of the processed foods. In particular, people who received ultra-processed foods chose to eat an average of 500 extra calories per day, and gained an average of 2 pounds per week. Yale's Dana Small suggests that the reason for this is that ultra-processed foods distort the brain's ability to accurately account for calories eaten, which causes the neurological system to continue sending hunger signals for a longer period of time. The University of Michigan's Kent Berridge adds that in rats, some gain wait from processed foods and others don't, but in the ones that gain wait, the brain's dopamine rewards system is changed. He adds that he thinks there is no single cause of rising obesity, and processed foods are only part of the picture. Purdue's Rick Mattes says its too soon to buy into the theory, saying that a small body of research has found an association between processed food and weight gain, but that a large body would be needed to make a persuasive case. h/t RealClear Science

  3. Limiting message forwarding on WhatsApp helped slow disinformation - Starting in January, WhatsApp reduced the limit of groups to which a message could be forwarded from 256 to 5. MIT's Kiran Garimella and colleagues joined thousands of public groups on whatsapp and scraped the data. What they found was that the spread of misinformation slowed by an order of magnitude, with 80% of messages halted within two days. However, 20% still went viral. Garimella suggests that whatsapp could be more effective by watching viral message, and taking a quarantine approach. Whatsapp said the change led to a decline of 25% in their overall message volume, but the article doesn't note whether the change had a similar suppression effect on valid, informative messages.

  4. No, it wasn’t a virus; it was Chrome that stopped Macs from booting - On Monday night, users started discovering that their Mac computers were unbootable, and on Wednesday, Google disclosed the cause. When installed on a Mac with system integrity protection disabled along with several other criteria, A new version of Chrome's keystone updater was damaging a crucial part of the Mac file system. Here is the process, from google, for recovering a damaged system:

    The process involves booting into recovery mode and then opening a terminal window, which among other ways can be accessed from the utilities folder. From there, run the following commands:

chroot /Volumes/Macintosh\ HD   # "Macintosh HD" is the default
rm -rf /Library/Google/GoogleSoftwareUpdate/GoogleSoftwareUpdate.bundle
mv var var_back  # var may not exist, but this is fine
ln -sh private/var var
chflags -h restricted /var
chflags -h hidden /var
xattr -sw com.apple.rootless "" /var

Then reboot.

  5. STEEM Cybersecurity Guidelines for University Programs to Align the Industry - In this post, @mrosenquist discusses the Cybersecurity Curricula guidelines for post-secondary degree programs. The guidelines were developed by a team of 300, including @mrosenquist, with a number of goals. According to the post, those goals include:

    • To describe a vision of proficiency in cybersecurity,
    • To define a structure for the cybersecurity discipline by developing a thought-model that defines the boundaries of the discipline and outlines key dimensions of the curricular structure,
    • To support the alignment of academic programs with industry needs in cybersecurity,
    • To involve a broad global audience of stakeholders through continuous community engagement during the development process,
    • To develop curricular guidance that is comprehensive enough to support a wide range of program types, and
    • To develop curricular guidance that is grounded in fundamental principles that provide stability yet is structured to provide flexibility to support evolving program needs.

    (A 10% beneficiary setting has been assigned to this post for @mrosenquist.)

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