Click HERE if you’re having trouble viewing the gallery on your mobile device.SAN FRANCISCO–The voice of public address announcer Renel Brooks-Moon echoed throughout AT&T Park, just as it does before every home game.“Now taking the field, your San Francisco Giants.”It’s the traditional cue for all nine starters to run out from the dugout, but ahead of game 162, only one Giants player emerged. Hunter Pence sprinted to his place in right field and received a standing ovation from an adoring …
SAN JOSE — Nearly a year ago to the day, Erik Karlsson made his debut in a Sharks jersey on the ice surface at SAP Center.Karlsson wasn’t playing, but between the first and second intermissions of the Sharks’ Sept. 22, 2018 preseason game against the Vegas Golden Knights, he skated out wearing the team’s new ‘stealth’ jersey — a nearly all black uniform with teal trim and white numbers and lettering.What had been a normal exhibition game turned into a more memorable experience, as Karlsson …
A 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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Share Facebook Twitter Google + LinkedIn Pinterest Well, we have no significant changes to our forecast. First, we will address the next 2 days, which in general, nobody cares about, giving the coming winter storm! Seriously, today and tomorrow will feature mild air again, although the northern part of the state continues to experience what we warned of to start the week…which was the potential for temps to be held in check by the cool snowpack. That cooling may be mitigated a bit more today and tomorrow as south flow picks up, but still, it definitely something to pay attention to. But, the next two days are as we have had them advertised…above normal in most areas, with some well above normal temps.Now, to what everyone REALLY wants to know about! We have made absolutely no change to our outlook for this coming winter storm. Track is still being handled in a tug of war fashion between two major computer models, and our thoughts are unchanged. Our next front should start to throw some affects into the state tomorrow evening and overnight, with those scattered showers continuing off and on through Friday morning. We are keeping liquid precipitation will range from a few hundredths to about a third of an inch over no more than 60% of the state. By Friday midday cold air will begin a full on assault from the west and northwest at the same time our low tracks up into the region along the cold front. Snow totals will depend heavily on the track of the low. One model takes the storm center more northeast, coming out of northern Mississippi, and the other farther east before heading north. The difference continues to be that of heavy snow in Indiana vs. heavy snow in Ohio. To be truthful, our bias at this time is more IN and west/NW Ohio, but we still are waiting for the storm track to be better defined. Snows can be quite significant out of this system, because it has tied into an ample moisture source, and the cold air is coming in with no major interference. The magnitude of the warm air push ahead of the system, and the strength of the winds will give us an indication that this storm is strong, and will have the potential to produce copious precipitation. . We will put out our official snow totals for this storm tomorrow (Thursday) morning. We still feel this has the potential to be an epic winter storm for a large swath of the Eastern Corn belt, across Indiana, Ohio or both. Gusty winds will produce blowing snow on top of this. The heaviest snows will be from noon Friday through noon Saturday, but wrap around snows can linger through Sunday in northern areas.Behind the system, cold air comes blasting back into the region, and stays through Tuesday. This will include low wind chills and a move below zero at least one night and perhaps more for true air temperatures.The rest of the 10 day forecast features an attempt to moderate temps slightly next Wednesday, but as we have previously stated, the moderation will not hold a candle to this week, Strong southwest winds fuel that moderating push ahead of our next weather system, triggering a brief, slight thaw. But, we look for scattered rain showers changing to snow late next week for Friday into Saturday, followed by cold air through the 21st. The extended 11-16 day forecast period brings another strong front and potential aggressive winter storm for the 22nd and 23rd, as a large, powerful low exits the plains and moves east/northeast. We expect this to bring another round of rains followed by significant snow and arctic air.
Have you ever been stuck circling the block waiting for a parking space to open up? The new ParkCirca space-sharing service might make that a thing of the past. Co-founder and CEO Chadwick Meyer told me how he was fruitlessly hunting for a space when he noticed how many private driveways had no cars in them. Why not let the driveway owners make some money from them, and save stress (and gas) for the drivers at the same time?That’s exactly what ParkCirca sets out to do. Driveway owners register when their space will be free and how much they want to charge. Drivers can then use an iPhone application to find available spots near their destination, and book them for the time they need. A typical charge might be $2 an hour, in which case an owner with a space available for just eight hours every week day could make up to $320 a month, without losing a place to park in the evenings or weekends.As a self-funded startup, Meyer and his team have just launched the service in San Francisco by walking around neighborhoods like the Haight, Cole Valley and Inner Sunset, handing out flyers and talking to people. He says the reaction has been very positive. “There’s traditionally been a lot of informal sharing between immediate neighbors. This gives people a tool to organize that, and extend the circle of trust a bit further too.” He also finds it remarkable how much has changed in the last decade of social technology, since his service relies on “communication between strangers,” requiring coordination that would have been almost impossible until recently.It’s still early days, but with several hundred users after just a week, there does seem to be interest. It also seems a natural complement to a car-sharing service like ZipCar, making your choice of parking spot at your destination as flexible as your choice of vehicle.Meyer pointed out that there are a lot of secondary benefits to the service too. It gives people a chance to help out other locals, to “be a neighborhood hero,” reduces the gas wasted circling the block, and removes the hassle of having to move your vehicle every two hours because of street parking regulations. There’s an active trade in garage and private space rentals here in San Francisco, but ParkCirca gives you the chance to park in multiple spots, rather than being anchored to a particular location.There’s no guarantees that their model will work, but as some who has recently moved to the city I really hope it does take off. Meyer is currently looking into raising angel funding to support his mission of “making urban life better for everyone,” and I wish him luck. How to Write a Welcome Email to New Employees? Why You Love Online Quizzes Growing Phone Scams: 5 Tips To Avoid 7 Types of Video that will Make a Massive Impac… Tags:#hack#Services pete warden Related Posts
With 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.