Claim of New Antifreeze Gene by Natural Selection Melts Under Analysis

first_imgA biochemist examines imaginative claims about natural selection creating a new gene.Did a New Gene Arise by Darwinian Selection?by Dr Ross Anderson*Dr. Anderson critiques a paper by Zhuang et al., “Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids” (PNAS, 13 Feb 2019), which claims a new antifreeze gene in Arctic cod arose by ‘fortuitous’ chance events and natural selection.“This paper is a concrete dissection of the process of a de novo gene birth that has conferred a vital adaptive function directly linked to natural selection.”Summary: The authors report here the putative assembly (evolution) of a gene encoding an antifreeze glycoprotein (AFGP) in cod fish. Comparing DNA sequences of AFGP-producing gadids with sequences from non-AGFP-producing gadids the authors believe they have identified a sequence in the non-AFGP gadids that doesn’t appear to code for a protein, but with a little imagination can be made into a gene which encodes an AFGP.Starting with Something, Not NothingSo, let’s see, here we have a fully formed, functional AFGP gene. As such it has all the components necessary for expression and regulation. We want to try and understand just how this gene could have arisen from a non-coding sequence; i.e., how it arose de novo. The authors recognize that most genes supposedly have arisen from pre-existing genes, but that new genes from non-coding sequences is rare, but theoretically possible. Reported here is a possible example of such a de novo gene.Examination of extant AFGPs reveals that they are typically composed of a short sequence of amino acids repeated many times; e.g., the tripeptide, Thr-Ala-Ala (threonine, alanine, alanine), repeated n times. Some of the Thr residues have been glycosylated; i.e., they have sugars added to a side-chain.The paper is an interesting read in that it reveals the very creative imagination of some scientists.Proteins are coded by triplet codons of DNA “letters” A, C, T, and G. (Illustra Media)Let’s use our creative imagination and see if we can construct a gene that encodes such a protein. First, we find some DNA sequences in gadids that are somewhat similar, but do not encode a protein; they are non-coding sequences. Compare these sequences with the target AFGP gene sequence and see what is needed to make these non-coding sequences match the target AFGP sequence. We notice that what we need is for the coding region to encode a polyprotein composed of the repeated amino acid sequence Thr-Ala-Ala. We find the DNA sequence GCA, which is an Ala codon, repeated 9 times to generate a 27-nucleotide (nt) sequence. In the target AFGP gene the Thr-Ala-Ala repeat is found bounded by two 27-nt (nucleotide) repeats. So, let’s propose that the sequence of 27 nucleotides (GCA repeated 9 times) in the “ancestral” sequence underwent a chance duplication event to generate two 27-nt repeats. Then propose a second chance duplication event to generate four such repeats.Blindly Aiming for the TargetExamination of the target AFGP amino acid sequence shows we need a Thr codon in the midst of the 27-nt repeats. Suppose we substitute an ‘A’ for the ‘G’ in one of the GCA sequences. The new 9-nt sequence would then read ACAGCAGCA which, when translated, would generate the required Thr-Ala-Ala sequence. Now that we have the appropriate coding sequence, we need to have it repeated as the target amino acid sequence, Thr-Ala-Ala, is repeated many times. So, let’s propose that this new 9-nt sequence is also duplicated many times.We also notice that in the functional AFGP gene there are scattered arginine and glutamine codons. Presumably when translated these will provide signals for a protease to hydrolyze the polypeptide into many shorter peptides which are the antifreeze proteins. To generate these two amino acid codons in a sea of GCA codons would require at a minimum two strategically placed substitutions in a GCA codon to generate either an arginine codon or a glutamine codon. The authors provide no explanation for how these substitutions nicely provide codons for only these two amino acids when codons for many other amino acids could be generated more easily with just one substitution. The magic is all done by chance and natural selection in six fortuitous steps. Here is the summary diagram of their model from the paper:Fig. 4Evolutionary mechanism of the gadid AFGP gene from noncoding DNA. The color codes of the sequence components follow Fig. 1. (A) The ancestral noncoding DNA contained latent signal peptide-coding exons with a 5′ Kozak motif, adjacent to a duplication-prone 27-nt GCA-rich sequence. (B) The 27-nt GCA(Ala)-rich sequence duplicated forming four tandem copies. (C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF. A proximal upstream regulatory region acquired through a putative translocation event. (E) A 1-nt frameshift led to a contiguous SP, a propeptide, and a Thr-Ala-Ala-like cds in a read-through ORF [open reading frame]. (F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.Signalling the BlindNow we have essentially constructed the coding region, but we’re not finished yet. All AFGPs are secreted proteins and as such require that a signal peptide sequence be attached to the coding region. The DNA sequence which encodes this signal has to be added to our coding sequence. It just so happens that the “ancestral” sequence has such a sequence in just the correct place with respect to the coding region. Only one problem, there is a single nucleotide which does not allow the signal sequence to be in the proper reading frame to the coding region. Let’s propose that this one nucleotide was deleted causing a reading frame-shift which then directly linked the signal sequence with the coding sequence. Interestingly, the authors indicate that DNA region encoding the signal sequence somehow develops an intron-exon structure, but no explanation is given.Promoting Chance to Commander of the FortuitousWe’re still not finished. We need a promoter region added to our new gene. Without a proper promoter, a gene will not be transcribed into an mRNA, and thus no protein product. The authors propose that “fortuitously”, a translocation event took place and the promoter from another gene was added in the exact location where needed. This proposed translocation also provided a 5′-untranslated region (UTR) in perfect alignment with the signal sequence as to save the reading frame generated earlier.All functional AFGP genes also have a 3′-UTR. One species of gadid lacks a 3′-UTR and is a putative pseudogene, suggesting that sequences in the 3′-UTR are necessary for expression. In the paper the authors add a 3′-UTR, but do not explain where it came from as it is not found in the putative ancestral sequence.Imaginative Storytelling Masquerading as ScienceThe paper is an interesting read in that it reveals the very creative imagination of some scientists. It is likened to examining a functioning car noting was is needed and going to a junkyard and auto parts store looking for all the pieces that could be cobbled together to make another functional car.Now, sequence comparisons can provide valuable information, however, when trying to construct an evolutionary story of how a gene might have arisen de novo, one must bear in mind that all is hypothetical as there is no real way to experimentally test the conclusions of such hypothesizing. In short, it amounts to just storytelling.The authors may have been able to come up with a more realistic explanation for the loss of function rather than try to explain a gain in function, but that would not have been as interesting or as much fun, and it certainly would not have been published.Note: for those interested in this subject, Dr. Cornelius Hunter, another biochemist, has critiqued the PNAS paper at Evolution News & Science Today. A related, but different claim about gene evolution from 2011 was analyzed by Shaun Doyle in the Journal of Creation (CMI).*About the authorDr. Anderson’s expertise is in the area of biochemistry and molecular biology. He has taught Biochemistry and helped to direct research projects of graduate and medical students at Baylor College of Medicine, Houston, TX. Dr. Anderson was a post-doctoral researcher in the Molecular Genetics Division of the Department of Ophthalmology at the Houston Neurosensory Center.Dr. Anderson was a member of both the undergraduate and graduate faculty at Lamar University, Beaumont, TX. There he taught and directed the research activities of undergraduates and Masters of Science degree candidates in Biology. Currently he is professor of biochemistry at The Master’s University in southern California.Dr. Anderson’s research interests include structure-function studies of DNA polymerizing enzymes and the synthesis and expression of synthetic human genes in bacterial hosts. He has authored or co-authored several publications in major, peer-reviewed journals. He is a member of the American Chemical Society and Sigma Xi Research Society.It’s an honor to have Dr Ross Anderson contribute this article to Creation-Evolution Headlines. Now, we end with a pictorial summary of Darwinian evolution by J. Beverly Greene. 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South African men: Lean in for women’s rights

first_imgSonke activists at a mobilisation in Delft organised to remember Queen, a 9-year-old girl who died on March 18th 2014, two months after being raped and set on fire. Although Queen identified her attacker, who was apprehended by police with fresh burn wounds and visible scratch marks, the case is not being prosecuted due to the failure of police to collect and present sufficient evidence. Sonke is working with community members and the police to ensure that Queen’s murder is properly prosecuted, and organises mobilisations to engage our community action team (CAT) and the Delft community to raise awareness around gender-based violence. (Image: Sonke Gender Justice)There’s no doubt masculinity is an important part of the identity of South African men. This is often not their choice. Ours is a country in which there is frequently enormous pressure on men, from all sides, to be men – to be manly.This is both a positive and a negative. The negative is that some men may wish to assert their masculinity by abusing those physically weaker than them – women and children. The positive is others embrace their masculinity in the spirit of Ubuntu. For them being a man is to be strong, protective, nurturing and supportive of others.Today Facebook COO Sheryl Sandberg launches a new global campaign as part of her established LeanIn initiative, which fights for the rights of women across the world. This time, Sandberg is asking men to join the fight. In this country, her call has been taken up by Brand South Africa. To mark International Women’s Day on Sunday 8 March, we urge our men to demonstrate how they celebrate and support South African women. This can be at home – creating stronger marriages and healthier, happier, more successful kids – and at work, for better team outcomes.Sandberg’s global campaign will be supported leaders ranging from top NBA athletes to influential CEOs and public figures such as Richard Branson, Warren Buffett, Melinda Gates, Arianna Huffington, Condoleezza Rice and Mark Zuckerberg.SOUTH AFRICAN MEN FIGHTING FOR WOMEN’S RIGHTSIn South Africa men need to reclaim their manhood as supporters of women, not abusers. There have been too many incidents where men have used their culture, physical strength and ability to earn more than their women counterparts to keep women in subservient positions.South African men must become role models to future generations of men by committing to being uplifting, caring, present and emotionally stable, for women to fully take their place, as equals, in our homes, communities and society.An example South African men leaning in for the rights of women is Sonke Gender Justice, a gender-rights civil society organisation set up and run by men.The organisation’s work includes initiatives such as the One Man Can, which encourages men to become actively involved in advocating for gender equality, preventing gender-based violence, and responding to HIV and Aids.Dumisani Rebombo runs the One Man Can project at Sonke’s new satellite office in the rural settlement of Bushbuckridge in Limpopo. The project forms part of a four-year randomised control trial being undertaken by Wits University, University of California, San Francisco and University of North Carolina, both in the US.It seeks to show how Sonke’s the project’s community mobilisation model can reduce levels of violence in this and other communities and ultimately reduce the levels of HIV infection in young women.According to Sonke, research conducted in 2009 by Chris Colvin indicated significant changes in short-term behaviour in the weeks following One Man Can activities. Twenty-five percent of respondents had accessed voluntary counselling and testing, 50% reported an act of gender-based violence, 61% increased their use of condoms, and over 80% talked to friends or family members about HIV, gender and human rights issues.New research by Shari Dworkin and colleagues shows further clear evidence that men taking part in these programmes change their attitude and behaviour in line with the objectives of One Man Can.This new qualitative research assessed OMC participants’ changes in masculine ideologies and health beliefs and behaviours. The study was conducted in two provinces, Limpopo and Eastern Cape, where the researchers conducted in-depth interviews with 60 OMC participants. Questions covered issues of gender relations and women’s rights, violence, relationships and sex, masculinity, fatherhood, gender and HIV risks, HIV prevention and testing, and community action teams.The research clearly shows that men who have participated in OMC activities afterwards embrace trends towards equality for women, understand their male identity differently and are more involved in household labour and child care.“A lot has changed in my life,” said one man who took part in the programme. “My childhood observations of a man as boss was wrong and before I attended OMC sessions; I continued to believe that it is the same wrong things that need to be done. But after some sessions and engagement in discussions with various people with various points of view, I then realised that it is wrong to treat women like they do not exist.”WOMEN HAVE BEEN WRONGEDThis year International Women’s Day on 8 March will highlight the UN Beijing Declaration and Platform for Action, a historic roadmap signed by 189 governments 20 years ago that sets the agenda for realising women’s rights.The Beijing initiative focuses on 12 critical areas of concern, and envisions a world where each woman and girl can exercise her choices, such as taking part in politics, getting an education, having an income, and living in societies free from violence and discrimination.UN Secretary-General, Ban Ki-moon, in his message for International Women’s Day 2015, said: “When we unleash the power of women, we can secure the future for all.”last_img read more

ABC Green With Envy After Wired Debuts iPad App [Update]

first_imgWhy IoT Apps are Eating Device Interfaces What it Takes to Build a Highly Secure FinTech … mike melanson Role of Mobile App Analytics In-App Engagement Related Posts center_img Tags:#Apple#mobile#news#web The Australian Broadcasting Corporation is said to be “leading the charge” in trying to get content on tablet devices, according to the Sydney Morning Herald, including, of course, Apple’s iPad, which is set to hit the market sometime next month. The ABC currently uses Flash, a software infamously not supported by the iPad, to stream video on its website.Just last Tuesday, Adobe and Wired Magazine announced a partnership, debuting a rather slick print-to-digital adaptation of the magazine. According to the report by the Herald, a senior executive at Adobe received an email from the ABC seeking a similar deal.Update: We mistakenly reported this as ABC, the American Broadcasting Company, not the Australian Broadcasting Corporation. The Herald quotes Abigail Thomas, head of strategic development at the ABC, as saying, the iPad will be more appropriate for entertainment than the iPhone.”It’s going to be an entertainment device. Whereas the iPhone is where you might get quick bites of news … with this [the iPad] you can imagine people sitting back on the sofa and enjoying something longer,” she said.While the iPad has received plenty in the way of criticism, including many seeing the lack of Flash as a huge detractor, it looks like some big names are working to get past this and get their content on the iPad. According the the Herald, a number of other companies, including the New York Times, Vanity Fair, GQ and Sports Illustrated, have also been working to bring their content to tablet devices, a number of which have been released at this week’s Mobile World Congress.Thanks to iPadInsider.com for the tip and lead image. The Rise and Rise of Mobile Payment Technologylast_img read more

With onset of rain, AES cases die down in Bihar

first_imgWith the onset of rains, no fresh AES case has been reported in Muzaffarpur district on Sunday even as the health department cracked its whip on a doctor who was asked to report for duty in the brain fever-affected district, but failed to comply.Dr. Bhimsen Kumar, a senior resident doctor at the Patna Medical College Hospital, had been directed to report at the SKMCH Muzaffarpur by June 19.“He failed to do so and the department has taken a serious note of the lapse. He has been placed under suspension pending a departmental inquiry upon conclusion of which further action may be taken,” Principal Secretary, Health, Sanjay Kumar said. Meanwhile, Sri Krishna Medical College Hospital (SKMCH) superintendent, Sunil Kumar Shahi said “AES is known to strike when the summer heat is at its peak and the incidences plummet no sooner than rainfalls lash the area. The same is happening this time and no child has been admitted during the day so far with the complaint even though AES patients, who have been nursed back to recovery, are being discharged continuously.”The Acute Encephalitis Syndrome (AES) outbreak, which according to the state health department has affected about 20 out of the 40 districts in the State, has afflicted more than 600 children since June 1, killing close to 140. The high number of deaths this year has been mostly attributed to hypoglycemia.last_img read more

a month agoN​orwich defender Byram: Our team spirit is sky high

first_imgN​orwich defender Byram: Our team spirit is sky highby Freddie Taylora month agoSend to a friendShare the loveNorwich City defender Sam Byram is praising the chemistry and unity of the squad as they navigate the Premier League.The newly promoted side got a famous win against Manchester City at the weekend, despite several first team members being out with injury.Byram believes that aside from quality coaching and preparation, the camaraderie in the squad makes it easier for them to push to achieve their goals.”The character and spirit is definitely one of the best I’ve experienced,” he said to the club’s official website. “You can see from everyone, the players on the bench and the players that even weren’t on the bench, everyone wants the team to do well.”That’s the main thing for the unity. Not one player is bigger than the team and you can see that today with the work rate, everyone has got each other’s back.”We had a bit of luck throughout the game but we defended unbelievably well and also had spells in the game where we played some really good football.”We always have belief that we could win. It’s Manchester City and they are an unbelievable team but we’ve got a squad here which is very close-knit.”If someone drops out, someone else can fill in. You know exactly what your job is and I think we showed today the spirit we’ve got and how good we can be.” About the authorFreddie TaylorShare the loveHave your saylast_img read more

Boy Those Toronto Blue Jays World Series Odds Went South Quick

Before any MLB playoff games were played, things were looking so good for Canada’s World Series hopes. (The country’s title drought in hockey gets all the attention, but no baseball champ has hailed from north of the border since 1993, either.) With odds of 19 percent, the Toronto Blue Jays had the best chance of winning the World Series of any team, according to our pre-playoffs MLB Elo ratings.Now? Not so much. The Blue Jays have lost the two first games to the Texas Rangers in their best-of-five American League Division Series. That’s changed their chance of winning it all — as well as everyone else’s.According to the latest Elo simulation of the rest of the playoffs — which includes the Rangers’ victory over Toronto on Friday afternoon but no subsequent results — the Blue Jays’ probability of breaking Canada’s winless streak is now just 5 percent: CHANCE THAT A TEAM WILL … Toronto Blue Jays15641001585 Los Angeles Dodgers1535100522411 New York Yankees15160000 TEAMELOMAKE LDSMAKE LCSMAKE WSWIN WS Kansas City Royals1538100331810 St. Louis Cardinals1549100502814 Texas Rangers1535100%85%43%22% New York Mets1523100482110 Pittsburgh Pirates15540000 Because they’re up 2-0 in their series versus Toronto, the Texas Rangers are now your World Series favorites, though that can and will change depending on what happens the rest of Friday. Houston Astros1528100673115 Chicago Cubs1558100502714 read more

Gattuso confirms Silva Kalinic will stay at Milan

first_imgAC Milan manager Gennaro Gattuso has confirmed that he intends to retain both Andre Silva and Nikola Kalinic for next seasonSilva joined the Rossoneri last summer from FC Porto in a €38m deal, but had only found the back of the net 10 times in his 40 appearances.Prior to joining Milan, the 22-year-old had scored 21 goals in 44 matches for Porto.Meanwhile, Kalinic completed a €25m move to Milan but he has appeared to be a mere shadow of the player he was during his time at Fiorentina and the Croatia international only scored six goals all season.Cristiano Ronaldo, JuventusSerie A Betting: Match-day 3 Stuart Heath – September 14, 2019 Considering there is a number of perfect starts so early in the Serie A season, as well as a few surprisingly not-so perfect ones….But, despite a lacklustre season from both of them, Gattuso intends to keep the pair at the San Siro.“Kalinic and Andre Silva? I hope that they will improve, Andre Silva has scored. All of you keep talking about an exit for them but we will hold onto them both, tightly,” said Gattuso, via Calcio Mercato.last_img read more

Arrizabalaga thanks de Gea for his advice

first_imgThe goalkeeper was transferred from Athletic Bilbao to Chelsea in the summer in a record £71.6 million buyYoung goalkeeper Kepa Arrizabalaga joined English Premier League side Chelsea during the summer after a £71.6 million transfer.The Spanish footballer left Athletic Bilbao after only two years with the Spanish La Liga club, to play in the EPL.And in his first time playing outside Spain, Arrizabalaga thanked Manchester United’s David de Gea, who helped him settle down.Roberto Firmino, LiverpoolVirgil van Dijk praises Roberto Firmino after Liverpool’s win Andrew Smyth – September 14, 2019 Virgil van Dijk hailed team-mate Roberto Firmino after coming off the bench to inspire Liverpool to a 3-1 comeback win against Newcastle United.“Every player settles into a new league in different ways,” he said to Sky Sports.“David is a team-mate with the national team and we get on really well. When I signed for Chelsea, he gave me some advice, telling me a bit about how it was for him when he came here.”“Of course, he has been here for years now and is playing at a fantastic level. We were at the World Cup together and had a good chat about the differences between Spanish and English football,” he added.“It’s a good thing to interact with a top goalkeeper who has so much experience in the Premier League.”last_img read more

DEC Conducts CleanUp From Small Spill On Kenai Lake

first_imgAccording to reports from the DEC, the contaminated soil was from a truck accident that took place back in February. The stretch of roadside was located near Quartz Creek Road intersects with the Sterling Highway. Facebook0TwitterEmailPrintFriendly分享The Department of Environmental Conservation worked to clean up roughly 4 yards of contaminated soil near Kenai Lake over the weekend. Alyssa Murphy with the ADEC: “The accident occured on February 26, and was reported to DEC February 29, by a concerned citizen. We went out on site that day that is was reported, and observed no stain on the ice or snow. But, a follow-up site inspection on April 13 revealed staining on the shoreline.” According to Murphy crews from the National Response Corporation arrived on scene the afternoon of April 13, to begin clean-up response efforts.center_img Murphy: “On April 17, a crew removed the stain areas using an excavator and 4 cubic yards of contaminated material were removed and taken to Anchorage for treatment and disposal.”   Murphy said DEC crews will be on scene this afternoon for another on-scene inspection and continue any necessary clean-up efforts.last_img read more

BTRC launches 100 to hear complaints

first_imgThe Bangladesh Telecommunication Regulatory Commission (BTRC) on Sunday launched its new short code number 100 in a bid to solve customer hazards and problems quickly.BTRC issued a direction in this regard cancelling the previous short code 2872.According to the direction, the operation of Complains for Telecommunication Service (CTS) call centre has gone easier with the new three-digit short code.BTRC secretary Sarwar Alam told UNB the previous number was changed as it was difficult for customers to recognize.The customers will be able to lodge complains from 9:00am to 5:00pm on working days.Along with the short code, phone number 01555121121 and website btrc@btrc.gov.bd was also available to lodge complain.last_img read more