Intelligent Design The Nylonase Story: How Unusual Is That?Ann GaugerMay 5, 2017, 2:44 AM Jane Goodall Meets the God Hypothesis A Physician Describes How Behe Changed His MindLife’s Origin — A “Mystery” Made AccessibleCodes Are Not Products of PhysicsIxnay on the Ambriancay PlosionexhayDesign Triangulation: My Thanksgiving Gift to All Congratulations to Science Magazine for an Honest Portrayal of Darwin’s Descent of Man “A Summary of the Evidence for Intelligent Design”: The Study Guide Requesting a (Partial) Retraction from Darrel Falk and BioLogos Ann GaugerSenior Fellow, Center for Science and CultureDr. Ann Gauger is Director of Science Communication and a Senior Fellow at the Discovery Institute Center for Science and Culture, and Senior Research Scientist at the Biologic Institute in Seattle, Washington. She received her Bachelor’s degree from MIT and her Ph.D. from the University of Washington Department of Zoology. She held a postdoctoral fellowship at Harvard University, where her work was on the molecular motor kinesin.Follow AnnProfile Share Evolution Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, of which this is the second, Discovery Institute biologist Ann Gauger takes a closer look.In an article yesterday, “The Nylonase Story: When Imagination and Facts Collide,” I described how some biologists claim that the enzyme nylonase demonstrates that it is easy to get new functional proteins. It has been proposed that nylonase is the result of a frameshift mutation that produced an entirely new coding sequence from an alternate reading frame. I showed why such a claim is false. Now I will explain what that means and something about the unusual properties of the nylB gene that caught molecular geneticist and evolutionary biologist Susumu Ohno’s attention.What are alternate reading frames? To answer that question, I first need to provide some background information. I will begin by defining some terms I used in yesterday’s post. DNA is composed of two anti-parallel strands of nucleotides. The order of the nucleotides in each strand is what specifies the information the DNA carries. The two strands, called the sense and antisense strands, run in opposite directions. Even though their sequences are complementary, with A always paired with T, and C with G, each strand carries different potential information.ATG GCA TGC ACC GGC ATT AG → senseTAC CGT ACG TGG CCG TAA TC ← antisenseBefore the information in DNA can be used, it must be copied into what we call messenger RNA. The sequence of one strand of DNA, usually the sense strand, is copied using the same base complementarity: G pairs with C, and A with U (U is used in place of T in RNA). We call that copying transcription. The message that has been transcribed from the DNA into that sequence of RNA is now ready to be translated into protein.Notice the language of information shot throughout these processes. The names for these processes were given by men fully committed to a naturalistic worldview, men such as Francis Crick and Sydney Brenner. Indeed, they were materialists one and all. Yet they saw the parallels between these processes and the human manipulation of text (language) or code (another form of language). The genetic code is the framework that determines the relationship between groups of nucleotides (codons), and the amino acids they specify. The code specifies how to translate the messenger RNA that has been copied or transcribed from the DNA, so that it can be translated into a new language, the language of proteins. Below is an illustration of the standard genetic code (source here, used with permission):Notice that the information in DNA is read in groups of three nucleotides (each group is called a codon), and each codon specifies a particular amino acid. Sometimes more than one codon can specify the same amino acid. For example in the top left corner, the table shows that UUU and UUC both specify the amino acid phenylalanine.The nature of the code is such that it matters where the first codon begins — the first codon to be read establishes the codon groupings going forward. In the table above the “start” codon is AUG (it also specifies the amino acid methionine). The sequence of codons is “read” by a cellular machine called the ribosome, which starts reading the RNA message at AUG, and then proceeds three nucleotides at a time to translate the message into amino acids. In the sequence below, for example, the first codon to be read would be AUG and that codon determines the frame in which of all the other codons are read.AUG GCA UGC ACC GGC AUU AGUNow here’s where it gets interesting. Potentially, DNA can be grouped into different codons, or frames, depending on where the ribosome starts reading. See below for an illustration. For example, the sequence could potentially be read with the groupings shown in frame one (ATG GCA etc.) or frame two (TGG CAT etc., if a proper ATG exists somewhere upstream), leading ultimately to a different amino acid sequences for each. In fact there are six possible ways to group the DNA into codons — three frames on the sense strand going left to right (labeled 1-3), and three frames on the antisense strand (labeled 4-6), going right to left. Below I have laid out the six possible frames for the sequence we began with, but with the alternate frames staggered, and the alternate codons separated by spaces. Notice the sequence stays the same — the only thing that changes from frame to frame is how the nucleotides are grouped. It’s the same sequence, but it could be read and translated differently in each frame. This is because each codon specifies a particular amino acid. Thus, each frame results in a completely different string of amino acids.frame 1 ATG GCA TGC ACC GGC ATT AGframe 2 TGG CAT GCA CCG GCA TTA Gframe 3 GGC ATG CAC CGG CAT TAGframe 4 TAC CGT ACG TGG CCG TAA TCframe 5 ACC GTA CGT GGC CGT AAT Cframe 6 CCG TAC GTG GCC GTA ATCThe codons TAA, TAG, and TGA are stop codons — they specify where the gene ends and protein translation stops. (For extra credit, can you find any ATG or stop codons in the above frames? They are there in both the forward and reverse direction. For more extra credit, can you use the code table to translate different frames, and demonstrate that each frame encodes a different protein?)So when Venema and others say that nylonase arose by a frameshift mutation that produced a novel protein 392 amino acids long, they are claiming that a completely new coding sequence with frame-shifted codons could generate a functional protein. How likely is that? Not very, given the rarity of functional proteins in sequence space (see my first post). And, as I have already shown in my first post, such an unlikely hypothesis is unnecessary. The nylB gene appears to be the product of a simple gene duplication followed by two stepwise mutations to increase nylonase activity.There is something special about the nylonase gene’s sequence though, something very odd. nylB has multiple large, overlapping (alternate) open frames that lack stop codons.How hard is it to get a gene with multiple reading frames?Let me explain. Roughly one in twenty codons are stop codons. A random DNA sequence will have stop codons about every sixty bases, and may or may not have a start codon. Usually the alternate frames of DNA sequences are interrupted by stop codons. Only the frame that actually specifies the correct gene will have no stop codons at all over a significant length. This system is actually very ingenious. The one frame that needs to be read and translated is identified by an ATG. The other frames will usually lack an ATG and/or will have several stop codons that interrupt their translation, thus preventing the cell from wasting energy on nonsense transcripts.According to the nylonase story, as told by Ohno and Venema and numerous others, a new ATG start codon was formed by the insertion of a T between an A and G, thus creating a new start codon after the original ATG, which shifted the reading frame for that sequence to that specified by the new ATG, and creating a completely different coding sequence and thus a new protein. Let us grant that scenario for the sake of argument. Normally such a shift would produce a new coding sequence that would be interrupted by stop codons, so the newly frameshifted protein would be truncated. Thus the only reason this frameshift hypothesis for nylonase is even remotely possible is because the sequence coding for nylonase is most unusual, and contains not one, not two, but three open frames Although frameshift mutations are ordinarily considered to be quite disruptive, at least in this case the putative brand new protein sequence would not terminate early due to stop codons.My point? The first step to getting a new functional protein of any length from a frameshift is to avoid stop codons. The odds of a random coding sequence having an open alternate frame, without stops, are poor. As a consequence, if a protein does have an open frame in addition to its coding sequence, it’s worth paying attention to. And it so happens that nylonase does have more than one open frame. The DNA sequence above illustrates the six frames, numbering them frames 1 through 6. Using that convention, frames 1 and 3 are read from the sense strand. Both have no stop codons over the length of the gene in the sense direction. Frame 4 on the antisense direction has no stop codons either. Frame 1 is the coding frame that specifies the nylonase protein, otherwise known as the open reading frame (ORF). It is defined by the presence of both a start and stop codon. The other two frames have no start codons or stop codons, so I’ll call them non-stop frames (NSFs). They are frames 3 and 4.The probability of a DNA sequence with an ORF on the sense strand and 2 NSFs is very small. Just exactly how small are the chances of avoiding a stop codon in three out of six frames? We set out to determine that by performing a numerical simulation using pseudorandom numbers to generate sequences at various levels of GC content. (By we I mean that my husband, Patrick Achey, who is an actuary, did the programming work, while I determined the parameters.) We chose to vary the GC content because sequences with a higher GC content have fewer stop codons. Remember, a stop codon always has an A and a T (TAA, TAG, and TGA are the stop codons) so having a sequence with a lower percentage of AT content will reduce the frequency of stop codons. Conversely, higher GC content makes the chances of avoiding stop codons and getting longer ORFs much greater, thus also increasing the chances of NSFs. The genomes of bacteria vary in their GC content, from less than 20 percent to as much as 75 percent, though the reason why is not known. One species of Flavobacterium has a genome with about 32 percent GC and 2400 genes — the precise values varies with the strain. The plasmid on which nylB resides is very different. It has 65 percent GC content. The gene encoding nylonase has an even higher 70 percent GC content, which is near the observed bacterial maximum of 75 percent.We chose to use a target ORF size of 900 nucleotides (or 300 amino acids) because it is an average size for a functional protein. Nylonase is 392 amino acids long; the small domain of beta lactamase, the enzyme my colleague Doug Axe studied, is about 150 amino acids long. The median length for an E. coli protein is 278 amino acids; for humans, the median length is 375.As expected, the simulation showed that the higher the GC content, the greater the likelihood that ORFs that are 900+ nucleotides long exist. At 50 percent GC, the average ORF length we obtained was about 60 nucleotides; most ORFs terminate well before 900 nucleotides. Indeed, in our simulation only two out of a million random sequences made it to 900 nucleotides before encountering a stop codon. As a result, we could not determine the rarity of NSFs at 50 percent GC — we would probably have to run the simulation for more than a billion trials to get any significant number of NSFs at all.Sequences at 60 percent GC gave 57 ORFs at least 900 nucleotides long out of a million trials, while sequences at 65 percent GC produced 404 out of a million, one of which also had an NSF.NSFs were much more probable for sequences that were 70 percent GC, like nylB. In our simulation 3,021 out of a million trials were ORFs at least 900 nucleotides long. That’s a frequency of .3 percent. Of those 3,021 ORFs, 86 had 1 NSF, and none had 2 NSFs. We had to run 10 million trials at 70 percent GC to see any ORFs with 2 NSFs. From those 10 million randomly generated sequences, we obtained 28,603 ORFs; 903 had 1 NSF and only 9 had 2 NSFs.Interestingly, at 80 percent GC we got a few sequences with 4 NSFs; but I don’t know of any bacterium with a GC content that high.Our simulation shows that multiple NSFs are very rare. The probability that an ORF 900 nucleotides long with 70 percent GC content will have two NSFs is 9 out of 28,603, or 0.0003. If these figures are recast to include the total number of trials required to get an ORF of that length and GC content and with 2 NSFs, the probability would be 9 out of 10,000,000 trials.A sequence like nylB is very rare. In fact, I suspect that for all cases where overlapping genes exist, in other words where alternate frames from the same sequence have the potential to code for different proteins, unusual sequence will necessarily be found. Likely it will be high in GC content. Could such rare sequences be accidental? I think that if we compare the expected number of alternate or overlapping NSFs per ORF, with the actual number we will find that there are more of these alternate open reading frames than would be predicted by chance.From another study of overlapping genes:Thus, bacterial genomes contain a larger number of long shadow ORFs [ORFs on alternate frames] than expected based on statistical analysis. Random mutational drift would have eliminated the signal long ago, if no selection pressures were stabilizing shadow ORFs. Deviations between the statistical model and bacterial genomes directly call for a functional explanation, since selection is the only force known to stabilize the depletion of stop codons. Most shadow genes have escaped discovery, as they are dismissed as false positives in most genome annotation programs. This is in sharp contrast to many embedded overlapping genes that have been discovered in bacteriophages. Since phages reside in a long term evolutionary equilibrium with the bacterial host genome, we suggest that overlooked shadow genes also exist in bacterial genomes.Indeed, a study of the pOAD2 plasmid from which nylB came indicates that there are potentially many overlapping genes on that plasmid. nylB′, for example, a homologous gene on the same plasmid that differs by 47 amino acids from nylB, also has 2 NSFs. These unusual and unexpected features of DNA have consequences for how we think about the origin of information in DNA sequences, as I shall discuss in the next post.Monday: “The Nylonase Story: The Information Enigma.”Photo: Nylon tire, 1967 AMC Marlin, by Christopher Ziemnowicz (Own work) [CC BY-SA 2.5, Public domain or CC BY-SA 2.5], via Wikimedia Commons. Origin of Life: Brian Miller Distills a Debate Between Dave Farina and James Tour Email Print Google+ Linkedin Twitter Share Email Print Google+ Linkedin Twitter Share Recommended Tagsamino acidscodonDennis VenemaDNAintelligent designnylonnylonaseopen reading framereading frameRNAsense and antisenseSusumu Ohno,Trending
The Tedeschi Trucks Band is underway with their annual NYC Beacon Theatre fall run, and as per usual, the band has been welcoming a number of special guests to the stage. Last night, they were joined by new Colbert bandleader Jon Batiste on “Bound for Glory”, “Don’t Think Twice” and finally an encore of a Sly Stone medley. During the encore, the band was also joined by Eric Krasno (Soulive/Lettuce) and Cochemea “Cheme” Gastelum (Sharon Jones and the Dap-Kings) to complete the powerful set.Check out photos from the memorable evening courtesy of photographer Chad Anderson (full gallery at the bottom).Setlist: Let Me Get By, Keep On Growing, Anyhow, Bird On A Wire, The Letter, Bound For Glory*, Don’t Think Twice*, Cry Me A River, I Want More, Midnight In Harlem, The Storm, I Pity The Fool, With A Little Help From My Friends, Enc: Sly Stone Medley*^(*) w/ Jon Batiste(^) w/ Eric Krasno and Cheme Load remaining images
Pinterest Share Email Since 1993, Boston Medical Center’s (BMC) Project ASSERT has offered alcohol and drug use screening, brief intervention and referral to treatment to patients treated for intoxication in the ED. In 2009, Project ASSERT, with support from Boston Public Health Commission and Massachusetts Department of Public Health, also began offering overdose prevention education and naloxone rescue kits to emergency department patients at risk for opioid overdose.In order to evaluate the feasibility of this program and describe the overdose risk knowledge, opioid use, and overdose response actions among patients receiving overdose prevention education, researchers from Boston University School of Medicine (BUSM) and BMC conducted a telephone survey of Project ASSERT patients between January 2011 and February 2012. Of the 415 patients who received overdose education during this time, 51 patients were surveyed. Of these 51 patients, 73 percent had received a naloxone rescue kit either in the emergency department or elsewhere, such as a detox facility, and approximately one third of the reported opioid use in the last 30 days.In addition, more than half had reported witnessing an overdose and calling 911 for help. Among those with naloxone rescue kits, about one-third administered naloxone during the rescue.“This study confirms that the emergency department provides a promising opportunity for opioid overdose harm reduction measures through overdose education and naloxone rescue kit distribution,” explained lead author Kristin Dwyer, MD, emergency physician at BMC. “Our program reached a high-risk population that commonly witnessed overdoses, called for help and used naloxone to rescue people, when available,” she added.Although the study was retrospective with a low response rate, the researchers believe this study provides useful information for planning larger studies and programs to further evaluate implementation, benefits and harms of overdose prevention efforts in EDs. Share on Facebook Emergency departments (ED) provide a promising venue to address opioid deaths with education on both overdose prevention and appropriate actions in a witnessed overdose. In addition, ED’s have the potential to equip patients with nasal naloxone rescue kits as part of this effort.These findings are from a study published in the Western Journal of Emergency Medicine, and is the first study to demonstrate the feasibility of ED-based opioid overdose prevention education and naloxone distribution to trained laypersons, patients and their social network.In the United States, deaths from prescription opioid overdose increased from 4,041 in 1999 to 16,651 in 2010. In 2011, an estimated 420,040 ED visits were related to overdose of prescription opioids and 258,482 heroin overdoses. LinkedIn Share on Twitter
BREAKING: Solicitor General asks SC to forfeit ABS CBN’s franchise FILE PHOTO – Tristan Tamayo/INQUIRER.netBangkok Glass claimed its lone win in the FIVB Women’s Club World Championship at the expense of PSL-F2 Logistics Manila, 25-16, 25-23, 25-20, Sunday at Mall of Asia Arena. The Thai club settled for 7th place while the host finished in eighth and last place. ADVERTISEMENT Chinese-manned vessel unsettles Bohol town Ashley Frazier led Bangkok Glass with 12 points while Thi Ngoc Hoa Nguyen and team captain Pleumjit Thinkaow added 11 points apiece.Jaja Santiago led the hosts with 11 points while Lindsay Stalzer added eight.Sports Related Videospowered by AdSparcRead Next MOST READ Brad Pitt wins his first acting Oscar as awards get underway Taiwan minister boards cruise ship turned away by Japan PLAY LIST 01:31Taiwan minister boards cruise ship turned away by Japan01:33WHO: ‘Global stocks of masks and respirators are now insufficient’01:01WHO: now 31,211 virus cases in China 102:02Vitamin C prevents but doesn’t cure diseases like coronavirus—medic03:07’HINDI PANG-SPORTS LANG!’03:03SILIP SA INTEL FUND Smart hosts first 5G-powered esports exhibition match in PH “Today we are really happy we won our last game here in the Philippines, but today was really difficult,” said Bangkok Glass head coach Porncha Kittipong. “Everybody played good and we’re really happy we did a good job today.”Kittipong was impressed with how PSL-F2 Logistics played them in the blocking department.FEATURED STORIESSPORTSGinebra teammates show love for SlaughterSPORTSWe are youngSPORTSCone plans to speak with Slaughter, agent BREAKING: Solicitor General asks SC to forfeit ABS CBN’s franchise Mainland China virus cases exceed 40,000; deaths rise to 908 Jett Manuel withdraws from PBA Draft to focus on UP 30 Filipinos from Wuhan quarantined in Capas Team ‘Trabaho’ scores championship title at the last leg of Smart Siklab Saya Manila PSL-F2 Logistics scored on seven of its blocks while Bangkok Glass managed just four but the Thai club enjoyed a 47-37 advantage in spikes.Moro Branislav, the head coach of PSL-F2 Logistics, fielded in his seven local players in the third set to finish the match. Ginebra teammates show love for Slaughter EDITORS’ PICK View comments Don’t miss out on the latest news and information. We are young
The Partnership is a voluntary association of communicators who have come together out of a sense of common responsibility to use the 2010 communication opportunity to create a better life for all.The partnership is not a legal entity – it is a partnership of communicators across sectors and creative and communication disciplinesAll communicators who wish to contribute to the furthering of the communication objectives of the Partnership can become part of this voluntary association.However, the Partnership does not provide access to the 2010 tournament terrain which belongs to FIFA, its sponsors, commercial affiliates and supporters, and the Organising Committee.The Partnership will form alliances with communicators across the African continent and in the diaspora so collectively we can use this opportunity to tell our stories of the African continent.The Partnership is championed by a Core Group of activist members broadly reflective of marketing, media, communication, advertising, public relations, market research, tourism, sports, government, public agencies and parastatals. Within the Core Group all sectors of society – labour, business, government, and civil society – are included.The Partnership will also drive engagements within the clusters which make up the Core Group – marketing and advertising, tourism, media and communication and arts and culture – for sustained coherence and coordination through exchange of information and sharing of strategy and plans.A Task Team drawn from the Core Group drives the work of the Partnership, and meets monthly.Government Communication and Information System and the International Marketing Council provide a joint secretariat to enable the work of the Partnership.The year long schedule of engagements culminates in an annual 2010 National Communication Partnership conference. Relationship to FIFA and the Organising CommitteeThe Organising Committee is a member of the 2010 National Communication Partnership.In 2005 the Organising Committee facilitated a meeting between representatives of the Partnership and FIFA. FIFA gave support to the approach of a partnership of communicators and its objectives of taking advantage of the World Cup opportunity to communicate about the country and continent.
This is where the random number generator comes in. To keep the account from spamming Twitter, “heroku run worker” runs once an hour. But instead of tweeting every time, it’s actually rolling a die. Every 8th time or so, it hits gold. As a result, your randomizer accounts should update about three times a day.Enjoy your new Twitter bot, and be sure to share it with me in the comments! Navigate to the heroku_ebooks folder on your computer, and open up local_settings_example.py. In a text editor, copy and paste the entire contents into a new document, which you’ll then save as local_settings.py.Fill in your Consumer Key, Consumer Secret, Access Token Key, and Access Token Secret in the allotted spaces. If you’re unsure which those are, here’s a hint: they’re in exactly the same order as they appeared on dev.twitter.com. Here are mine as they appear in order, though blurred out. Don’t ever share secret keys—that’s gotten Amazon Web Services customers in trouble! A friend of mine, who knows about my love of esoteric Internet phenomena, built @LaurenInEbooks as a gift. It’s inspired by @horse_ebooks, a Twitter account so famous for its poorly computer-generated tweets that it got profiled in the New Yorker, which revealed that it had gone from a weird spam effort to sell ebooks into a mysterious art project.Horse_ebooks is an old joke by now. But it’s not too late for you to get in on this bizarre genre of word art. A computer-generated account which serves as your own personal Twitter bot Frankenstein is always fresh and funny.Plus, for beginning coders like me, this project is a great way to dip your toe into Python and Ruby while sharpening your Git skills—and at the end, get a hilarious little bot for your troubles. See also: GitHub For Beginners: Don’t Get Scared, Get StartedSome of my coworkers wanted in join in on the fun, so I decided to buildthemsome Twitter bots, too. However, I found the starter script I chose to use, Heroku Ebooks, significantly difficult to follow. Building on top of it, I decided to create a tutorial anybody can use.A caveat: I built this tutorial on a Mac using its Terminal app, software which provides direct access to running software programs. I have not tested this tutorial for Windows machines, but if you need help, start with GitHub’s Windows instructions. It took me three tries to perfect the process. By the third time, building a bot took me only 20 minutes to complete! Here’s how to easily build your own random Twitter bot—and learn a little code at your friends’ expense. Note: An astute reader has reported that this tutorial won’t work properly if the source’s Twitter account has fewer than 3,600 tweets. So be sure to build a bot that picks on somebody who tweets a lot! Set Up A Twitter Account If you follow my standard Twitter account, @LaurenInSpace, you’re missing out on the good stuff. @LaurenInEbooks is a computer-generated stream of garbled tweets that are often far more on point than what I actually have to say. 7 Types of Video that will Make a Massive Impac… You’re going to need a place for these tweets to go, so build a new Twitter account with a funny name. If you add “ebooks” to the end, @horse_ebooks fans will instantly get the reference, but you can choose any variation you like. In order to verify the account, you’ll need an email address that isn’t already being used by Twitter, so I’d suggest a secondary email you rarely use. I just generated a new email address I’ll probably never check again over at my hosting service, Bluehost, but you can also sign up for a new one on Gmail, Yahoo Mail, or Outlook.com.This new Twitter account also MUST have a mobile number connected to it. I used Google Voice, since they give you your first number for free. If I needed another I might have used Twilio, which also gives you your first number for free.If you need to create a lot of accounts, Twilio will cost $1/month, which can add up fast. And I should also note that while Twitter allows you to create parody accounts, “mass account creation” is against the rules. Twitter also has rules on automated accounts which you should follow. So don’t go crazy with your bots. This is also a good time to make a profile image. For @SelenaEbooks, I inverted the colors on her face to make a bizarro version of her Twitter image. I’m sure she just loves it.Set Up A Twitter Developer AccountWhile still logged into your new Twitter account, navigate over to dev.twitter.com. The first thing you want to do is create a new app. For convenience, use the same name as your new account. If you get an error that the program is unable to write to Twitter, make sure you gave it read and write permission back in dev.twitter.com. That’s an early mistake I made.This program works as a random number generator. As a result, it seems like it takes forever to get “heroku run worker” to deliver anything. Ugh. If you get REALLY frustrated, you can raise its chances from 1 in 8 to 1 in 4, etc. on the ODDS line in local_settings.py. Tags:#@horse_ebooks#automation#DIY#Friday Fun#Git#GitHub#Heroku#learn to code#tutorial#twitter#Twitter bots We’re going to create this app by installing a free app-developer program called Heroku. First, go to Heroku.com and sign up for an account. I know you may be reluctant to do this, but you’re going to need to have a “verified” account, and that means inputting your credit card information. I wish Heroku didn’t do it this way, but it’s necessary for later, and I’ve never been charged a cent. Now that we’re signed up, here’s the problem: Our heroku_ebooks program files are on our computer, not the Web. So we need to use Heroku on our computer. Download Heroku Toolbelt in order to do that. Once Heroku is installed, go to your command-line window—in Terminal on the Mac, in the Windows command line on Windows machines. We need to build a Heroku app, but we want to make sure it builds in the right place. cd heroku_ebooks Once inside, we need to start up Git. For me, this was the most complicated part of the project. I kept getting an error where Git was unable to find my app, unless I typed exactly the following:git initgit add .git commit -am “Add all files”heroku create –stack cedargit push heroku masterWith the first three lines, we’re setting up a fresh initialization of Git in this folder and told it to include and track the documents already located in this folder.Then, we’re using the “Heroku create” command to build a new app on the cedar stack. Celadon Cedar, or cedar for short, is a deployment environment for Heroku. It lets Heroku access libraries that allow it to understand Python, Ruby, and any other language you want to build apps with.Heroku has a nature-based naming convention, and it’ll randomly assign a name to your app based on that, in this case “damp-spire-9517.” You never have to change the name of the app since it won’t show publicly—it’ll just be how you identify it in your Heroku account.In this screenshot, I’ve moved on from making fun of my colleague Selena Larson and tackled my boss, Owen Thomas, with @OwenEbooks. With the final line, we’re pushing out all our heroku_ebooks files, including the local_settings.py file we built, to our Heroku app’s home on the Web. Heroku stores them in its servers and will run the app for us. Note: if you made a mistake in local_settings.py and need to update it, it’s just like doing any other update in Git. First, change the file, save, and exit. Then, back on the command line:cd heroku_ebooksgit add local_settings.pygit commit -am “Update local_settings.py”git push heroku masterYou shouldn’t get this error if you’ve done everything the way I said, but the most common error is going to be: ! Push rejected, no Cedar-supported app detectedThis means it can’t find a Heroku app in the heroku_ebooks folder. Remove and reinitialize Git with:rm -rf .gitgit initgit add .Then try once more to create a new Heroku app in the folder. If it is working, you’ll get this notice instead:—–> Python app detected Once it’s done pushing changes to the master branch, you can test to see if it’s working:heroku run workerThis will give you one of two responses: 1 No, sorry, not this time. In this response, “1” could be any number 1 through 7, or, an actual tweet: Schedule Tweets For The Future Note that I set both T/F (true/false) variables to FALSE. If the first one isn’t set this way, it won’t be able to write to Twitter. Sign Up For And Install Heroku Once you’ve got your first tweet—a step you really should take to verify everything’s working—you’ll want to schedule “heroku run worker” to run at regular intervals during the day, so you don’t have to manually tweet for it yourself.Type:heroku addons:add scheduler:standardIf you didn’t “verify” your Heroku account with a credit card, this command won’t work. Go get that credit card! Otherwise, type this once the scheduler installs:heroku addons:open schedulerIt’ll take you to a page on Heroku where you can configure the program. Name it “worker,” and set the frequency to “hourly.” Hit save. Whenever you are working on a coding project, you are always standing on the shoulders of giants. In this case, we’re borrowing an open source Ruby and Python script that GitHub user Tom Meagher has saved in a repository. You need a copy of Tom’s repository on your computer. The easiest way to do this is to hit “Clone In Desktop” or “Download Zip.” Either way, you want to take the resulting folder, which will be called heroku_ebooks, and store it in the very top directory of your computer.Update Your Settings When it says to list the account, don’t write out the full Twitter account URL (twitter.com/selenaebooks) or even put an @ in front of the Twitter username (@selenaebooks). Here’s how I did the @SelenaEbooks account: Growing Phone Scams: 5 Tips To Avoid Related Posts Why You Love Online Quizzes How to Write a Welcome Email to New Employees? Once you’ve named and created your app, you’re going to immediately want to adjust its permissions to “Read and Write.” In order to post to Twitter from a program, it needs to have a mobile number connected to the account—which is why we needed to create one earlier. Next, go to the API Keys page and click “Generate my Access Token,” and keep the window open while it works. You’ll need those keys and tokens in just a few minutes. Clone The GitHub Repository lauren orsini
In today’s Big Story podcast, it’s 2019. By now plenty of Canadians have humiliating results in Google searches for their name. But do we need a process for making those listings disappear?The European Union has one—it’s called the Right To Be Forgotten. And there’s currently a debate in public and in the courts, over whether or not Canada needs such a framework. But if we did have it, who would get to exercise that right? Who would decide if a piece of information should vanish from Google or not? And … should we even be allowed to hide true results about us online?GUEST: Michael Geist, Law Professor, University of Ottawa, online privacy specialistYou can subscribe to The Big Story podcast on Apple Podcasts, Google and SpotifyYou can also find it at thebigstorypodcast.ca.
Arsenal great Robert Pires believes Alexis Sanchez made a big error in choosing to leave the club for Manchester United and ponders whether he will have to move to another club soonThe Chilean forward has managed just four goals and six assists in 26 appearances for United across all competitions since arriving from Arsenal in January.Manager Jose Mourinho hailed Sanchez’s signing at Old Trafford as a major coup back then, but the 29-year-old could be out of the club by the New Year.And Pires feels he knows exactly where Sanchez went wrong.“Alexis was very good, he’s an excellent footballer, but I also got to know him as a person and I can say that I loved knowing him, he is a friend,” Pires told El Mercurio.“He stands out for his professionalism and that helped Arsenal to win several titles.“Honestly, it surprised me. For me, Sanchez had to stay at Arsenal, where he was one of our stars.“I don’t know if he could say no to United, but I think the style of play of the London club suits his performances better. But you have to respect his decision.”Alexis Sanchez 2014/15 was something else pic.twitter.com/Xv4OdsOwzDMaguire says United need to build on today’s win George Patchias – September 14, 2019 Harry Maguire wants his United teammates to build on the victory over Leicester City.During the summer, Harry Maguire was referred to as the ultimate…— Rk (@RkFutbol) October 16, 2018The former France international did, however, suggest that Sanchez would have benefited working under Pep Guardiola at Manchester City rather than Mourinho.“Yes, he’s going through a complex moment. The relationship with the manager is always important, but it’s notable that there are complications between Jose Mourinho and him,” added Pires.“When you’re a United manager and you have players like Paul Pogba and Sanchez, you have to take care of them, because in the end the only important thing is for the team to win.“When there are problems, the most important and complicated thing, at the same time, is to sit down to talk and say things face to face.“Sanchez doesn’t deserve to be on the bench or stay at home. We’ll see if he finds a solution in January, because he is not playing and he has to do it, since he is a wonderful footballer.“Mourinho and Josep Guardiola are two coaches who know how to win and conquer titles, but now, City’s way of playing is higher than United’s and it could be that if Alexis went to Pep’s team his situation would be different.”Liverpool legend Jamie Carragher even suggested Sanchez has become the new Fernando Torres of Chelsea.
The soft actuator maintained a flat and unwrinkled form under ambient conditions with relative humidity, while bending in response to increasing/decreasing humidity in the environment, which Cai et al. quantitatively analyzed. They noted excellent actuator performance and controllable bending angles in a variety of humidity levels. The scientists next investigated the electrical actuation of the device by connecting an MXene-cellulose strip to two copper wires. The bending angle almost linearly decreased with increasing electrical power, while the soft actuator only required a low voltage to achieve extreme actuation. Compared to humidity-based actuation, the scientists achieved larger bending angles with electrothermal actuation. The scientists also recorded temperature variation and binding angles of soft actuators using near infrared (NIR) light irradiation. They observed remarkable synergistic actuation motion of the MXene/cellulose composite material, in contrast to poor actuation performance of the individual components. Based on the observed optical absorption, photothermal conversion and electrochemical actuation, Cai et al anticipate the use of these composite smart soft actuators in photo-responsive functions. Cai et al. further investigated the photoinduced mechanical forces of the material under NIR light irradiation on a mechanical analyzer. The actuation process of MXCC/PC was rapid and reversible. The scientists studied the structural changes of the MXCC/PC and MXene/PC actuators under different intensities of illumination using X-ray diffraction (XRD) measurements to show amorphous character of cellulose and PC membrane. They investigated the mechanical behavior using finite element modelling methods (FEM) to further understand the actuation process of the composite material. The modeling results agreed with the experimental outcomes in the study. To demonstrate programmable actuation behavior, the scientists developed a series of sophisticated configurations. Including a double folding U-shaped actuator, trefoil arch-shaped actuator and self-blooming flower where the petals opened and bloomed before NIR irradiation to close rapidly on exposure to NIR. Additionally, the scientists explored a variety of smart devices such as worm-like robots, smart switches, an encryption device as well as IR dynamic display and camouflage to extend the primary concept. Furthermore, Cai et al. constructed a smart switch by patterning cross-shaped MXCC on the PC membrane, which they controlled using wireless NIR light. Based on the principles, the scientists also formed an open electrical circuit to switch on/off a smart watch using NIR light. For data encryption, based on the programmable MXene-cellulose ink, Cai et al. engineered a desired pattern and conveyed the information by local heating using NIR light or electricity. The information was only readable using IR and invisible to the human eye, providing better suited information encryption beyond machine readable barcodes and QR codes. The ability to integrate diverse functionalities into one system to achieve camouflage, display and actuation is important and useful in multiple disciplines. These devices confirmed the possibility of using MXCC/PC membranes to serve multiple functions in smart soft systems including information encryption, camouflage and thermo-responsive behavior. , Science © 2019 Science X Network Explore further Journal information: Science Advances Citation: Bioinspired MXene-based actuators for programmable smart devices (2019, July 18) retrieved 18 August 2019 from https://phys.org/news/2019-07-bioinspired-mxene-based-actuators-programmable-smart.html A variety of environmental stimuli such as humidity, temperature, electricity, light and pH can trigger physical alterations of these materials. But it is presently difficult to enhance the speed of actuation and scale-up shape changes due to poor mechanical and thermal instability that restrict their capabilities. Building a smart actuator that responds to diverse stimuli such as humidity, electricity, heat or light with fast actuation, large-shape deformation, programmable adaptability and robust stability is therefore highly desirable. To build new and improved material properties, the materials scientists must therefore explore previously unidentified combinatorial materials and rationally design device configurations to invent high-performance actuators. The elaborate structure, components, and actuation mechanism of the MXene-cellulose–based actuator. (A) Photograph of a natural leaf. (B) Schematic diagram of a leaf structure. (C) Schematic diagram of the MXCC/PC bilayer-structured actuator, which is composed of MXCC and a PC filter membrane. (D) Actuation mechanism of the MXCC/PC bilayer-structured actuator. Macroscopic and microcosmic (involving H bonds) structure changes of the MXCC/PC bilayer-structured actuator in response to hygroscopic and thermal stimuli simultaneously (both hygroscopic and thermal actuation processes are controlled by electrical and NIR light actuation). Scanning electron microscopy images of the MXCC (E) and the PC filter membrane (F). Contact angle measurement of the MXCC (G) and PC filter membrane (H). (I) Transmission electron microscopy image of the 2D MXene nanosheet (inset: SAED pattern). Credit: Science Advances, doi: 10.1126/sciadv.aaw7956 During photosynthesis, natural leaves with elaborate architectures and functional components can harvest and convert solar energy into chemical fuels that are converted into energy. The biological energy production has provided materials scientists a new bioinspired paradigm to produce many autonomous systems, including light-triggered motion. In a recent report, Guofo Cai and co-workers at the departments of Materials Science and Engineering, Astronautic Science and Mechanics, and Chemical Engineering, developed an unprecedented bilayered actuator base on MXene (Ti3C2Tx)-cellulose composites (MXCC) and polycarbonate (PC) membranes. Programmable soft actuators show the great potential of soft robotics , Advanced Materials Representative programmable motions for the MXCC/PC bilayer-structured actuator. (A) Double folding U-shape actuator. (B) Trefoil arch–shaped actuator. (C) Self-folding box. (D) Self-blooming flower. Green dashed lines in (C) and (D) (left diagram drawing) are the slight creases created on the bottom of the box and flower to make the self-folding box and self-blooming flower work well under NIR irradiation. (Photo credit: Guofa Cai, Nanyang Technological University.) Credit: Science Advances, doi: 10.1126/sciadv.aaw7956 A real-time digital camera video of the MXCC/PC bilayer-structured actuator upon sequential on/off NIR light irradiation. Credit: Science Advances, doi: 10.1126/sciadv.aaw7956 More information: Guofa Cai et al. Leaf-inspired multiresponsive MXene-based actuator for programmable smart devices, Science Advances (2019). DOI: 10.1126/sciadv.aaw7956 M. Ma et al. Bio-Inspired Polymer Composite Actuator and Generator Driven by Water Gradients, Science (2013). DOI: 10.1126/science.1230262 Xili Lu et al. Liquid-Crystalline Dynamic Networks Doped with Gold Nanorods Showing Enhanced Photocontrol of Actuation, Advanced Materials (2018). DOI: 10.1002/adma.201706597 R. H. Baughman. MATERIALS SCIENCE: Playing Nature’s Game with Artificial Muscles, Science (2005). DOI: 10.1126/science.1099010 The new composite materials, rational design and low-cost fabrication introduced in the study, alongside synthetic strategies implemented by the scientists, will make the MXCC/PC membrane systems accessible for broad scientific and engineering fields. In this way, Guofa Cai and co-workers developed and established a new class of multiresponsive materials and devices with unprecedented integration of multiple properties inspired by multifunctional biological structures. The MXCC/PC membrane systems mimicked crucial features of a natural leaf from the microstructure to photosynthetic capabilities, which included energy-harvesting and conversion. The bilayer actuators showed strong features, similar to state-of-the-art multiresponsive actuators. The explored materials and advanced systems can be further developed to establish novel possibilities for revolutionary technologies in the fields of soft robotics, information encryption and IR dynamic display. LEFT: Mechanical performance and motions of the MXCC/PC bilayer-structured actuator caused by NIR light. (A) Typical static force and strain changes of the MXCC- and cellulose-based actuators during one actuation cycle when NIR light illumination was turned on and off (50 mW cm−2). (B) Plot of the static force and strain of the MXCC- and cellulose-based actuators as a function of time for five consecutive NIR light on and off cycles, indicating the reversible, stable, and rapid actuation process. (C) Static force changes of the MXCC-based actuator under different NIR illumination intensities (from 5 to 200 mW cm−2). (D) Bending angle of the MXCC-based actuator under different NIR illumination intensities (from 5 to 200 mW cm−2). RIGHT: Structure change under different NIR illumination intensities and mechanical modeling. (A) XRD patterns of MXCC- and MXene-based actuators under different NIR light illumination intensities (solid lines, MXCC-based actuator; dashed lines, MXene-based actuator). (B) Corresponding d-spacing of the MXCC- and MXene-based actuators under different NIR light illumination intensities. (C) Simulated and experimental results of the MXCC-based actuator. (D) Simulated results of the MXCC-based actuator under NIR light illumination. Credit: Science Advances, doi: 10.1126/sciadv.aaw7956 A real-time digital camera video of smart switch upon sequential on/off NIR light irradiation. Credit: Science Advances, doi: 10.1126/sciadv.aaw7956 MXene (Ti3C2Tx) used in the present work belongs to a new family of liquid-crystalline, two-dimensional (2-D) metal carbides with excellent electrical conductivity, thermal conductivity and photothermal conversion to form multiresponsive and potentially high performance actuators. Only a single example currently exists of the use of MXene as an electrochemical actuator. In the present work, therefore, Cai et al. aimed at using MXene as a multiresponsive soft actuator to explore leaf-inspired, sophisticated architecture for simple actuation, coupled with synergistic functional components. Inspired by the biological architecture and photosynthetic mechanism of a natural leaf, Cai et al. designed an asymmetric, bilayered soft actuator using single-crystal, 2-D MXene nanosheets to harvest electric or light energy for conversion into thermal energy. For this, they used biocompatible, cellulose nanofibers to form the vein skeleton for rapid leaf-like shape changes alongside polycarbonate (PC) filter membranes to form the stomata and epidermis for water insertion and extraction to or from the MXene-cellulose composites (MXCC). The scientists confirmed the increased absorption of water in MXCC due to the presence of cellulose using Fourier Transform Infrared (FTIR) spectra. Using selected area electron diffraction (SAED) patterns, they detected the presence of MXene as a hexagonal structure and single crystallinity without defects at the nanometer scale. The device mimicked the sophisticated architecture of a leaf and showed energy-harvesting and conversion capabilities similar to photosynthesis. The bilayered actuator contained highly desirable features including; multi-responsiveness, low-power actuation, fast actuation speed, large-shape deformation, robust stability and programmable adaptability—well suited for modern soft actuator-based smart systems. Cai et al. believe these adaptive soft systems will be attractive as revolutionary technologies to build soft robots, smart switches, for information encryption, infrared dynamic display, camouflage and temperature regulation. They envision additional uses of the technology to develop human-machine interfaces such as haptics. The study is now published in Science Advances. Materials scientists have studied materials and devices that dynamically change shape, size and electrical/mechanical properties in response to external stimuli for a variety of applications. Such devices have important functions as actuators, artificial muscles, in robotics, as energy generators, sensors and smart curtains. Scientists have devoted substantial efforts to develop smart actuators based on a variety of active materials such as carbon nanotubes and graphene, shape memory polymers, gels, conjugated polymers and liquid crystal elastomers as well as ceramics and alloys. This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.