Minimal Cell Challenges Naturalism

first_imgOrigin of life theorists face a much higher “Mount Improbable” seeing a minimal cell with 473 genes.Craig Venter’s team has published results of their latest attempt to strip down a living cell to bare essentials (the organism must be free-living, not parasitic). They’re calling it “Syn 3.0.” After years determining what a version of Mycoplasma mycoides bacterium could do without, they came up with a “synthetic” cell containing 473 genes deemed essential. They could not determine the function for 149 of the genes.It’s the talk of the town in science news circles, because Syn 3.0 is much more complex than any proposed protocell emerging from a chemical soup. On his blog Darwin’s God, Cornelius Hunter remarks, “Mycoplasma mycoides Just Destroyed Evolution.” Here are some media headlines:Artificial cell designed in lab reveals genes essential to life (New Scientist)Synthetic bug given ‘fewest genes’ (BBC News)Creation of minimal cell with just the genes needed for independent life (Science Daily)‘Minimal’ cell raises stakes in race to harness synthetic life (Nature News)Tiny Artificial Life: Lab-Made Bacterium Sports Smallest Genome Yet (Live Science)Microbe with stripped-down DNA may hint at secrets of life (PhysOrg)Science Magazine published the original research by Hutchinson, Venter et al.  Commenting on the paper for Science, Robert F. Service says the organism has “fewest genes” but “many mysteries.” Venter’s team first tried to strip down their earlier bug, Syn 1.0, but the complexity of the cell stumped them.In their current work, Venter, along with project leader Clyde Hutchison at JCVI, set out to determine the minimal set of genes needed for life by stripping nonessential genes from Syn 1.0. They initially formed two teams, each with the same task: using all available genomic knowledge to design a bacterial chromosome with the hypothetical minimum genome. Both proposals were then synthesized and transplanted into M. capricolum to see whether either would produce a viable organism.“The big news is we failed,” Venter says. “I was surprised.” Neither chromosome produced a living microbe. It’s clear, Venter says, that “our current knowledge of biology is not sufficient to sit down and design a living organism and build it.”They started over with a “top-down” approach. Beginning with Syn 1.0, they systematically stripped out anything the bacterium could live without. They got it down to 473 genes, about half the size of their Syn 1.0 organism.The big news is that so many genes are essential, and that 149 of the essential genes have unknown functions. New Scientist quotes a biochemist in the UK:“Finding so many genes without a known function is unsettling, but it’s exciting because it’s left us with much still to learn,” says Alistair Elfick, a bioengineer at the University of Edinburgh, UK….“If we’re already playing God, we’re not doing a particularly good job of it,” Elfick says. “Simply streamlining what’s already in nature doesn’t seem very God-like and, if anything, is a very humbling exercise.”Venter also felt the humility vibes, according to Live Science:“We’re showing how complex life is even in the simplest of organisms,” said Craig Venter, founder and CEO of the J. Craig Venter Institute (JCVI), where the study was completed. “These findings are very humbling in that regard.”From an intelligent design perspective, Ann Gauger explains in Evolution News & Views why this organism (and any protocell) is irreducibly complex:All of this leads to an obvious question. This little bacterium has to be able to copy its DNA, transcribe and translate it into protein, plus be able to coordinate all the steps involved in cell division. It has to be able to make all the things it can’t get from its environment. That’s a lot of information to be stored and used appropriately. Hence 473 genes.This puts pressure on the origin-of-life field.But where did the cell come from in the first place? It’s a chicken-and-egg problem. Given the number of things the cell has to do to be a functioning organism, where does one begin? DNA or RNA alone is not enough, because protein is needed to copy the DNA and to carry out basic cellular processes. But protein is not enough by itself either. DNA is needed to stably inherit the genetic information about how to make proteins.It’s like a car, Gauger says. It needs “engine, a transmission, a drive shaft, a steering wheel, axles and wheels, plus a chassis to hold it all together,” to say nothing of gas and a starter. If you get only one or two of those things, you have a piece of junk, not a transportation machine.Take just protein synthesis. An article on PhysOrg explains that having the building blocks is not enough. The protein recipe “requires precise timing” as well. The steps are “precisely choreographed” analogous to a ballet or a recipe in the kitchen.In fact, details about the splicing step just came to light in a paper in Science Magazine. Just one subcomplex “must dock onto the rest of the spliceosome and hints at the structural changes the complex must go through to form the mature spliceosome.” This matures the messenger RNA before it goes into the ribosome to be translated into a protein. Summarizing the find for Science, Jamie H. D. Cate calls it a “big bang in spliceosome structural biology.” Splicing occurs in eukaryotes, which evolutionists think evolved later than bacteria. Even so, numerous proteins are involved in handling DNA and RNA in the simplest living organisms, including Syn 3.0.According to PhysOrg, lead author Hutchinson said that the genome in their minimal cell is “as small as we can get it and still have an organism that is … useful.” Even so, the bacterium lives in the comparative comfort and safety of the lab. Would it survive in the wild? Most cells live in ecological communities with other cells in complex food webs. How would the first protocell get along in a sterile world before life?Live Science posted a somewhat humorous slide show about theories for the origin of life – humorous, because none of them work. Opening with Darwin and Oparin’s speculation about a primordial soup, Charles Q. Choi’s list includes:Electric spark (Miller experiment)Clay (Alexander Cairns-Smith’s favorite hypothesis)Deep-sea vents (Michael Russell’s model)Chilly start (obviously at odds with the above models, but needed to protect from UV rays)RNA World (a dead idea according to leading theorists)Simpler beginnings (“garbage bag world” or “lipid world”)Panspermia (Francis Crick’s escape; it just pushes the question farther out to space)Each of these models has its supporters and detractors. Some are mutually exclusive. One party tries to start with metabolism, but no genetics. Another tries to start with genetics (RNA World), but no protein. Some like it hot, some like it cold. RNA was the leading hope that a molecule could emerge by chance that could begin evolving by Darwinian natural selection. Without natural selection, all agree that lucky accidents would have to occur by chance.Susan Mazur rubbed shoulders with the leading origin-of-life theorists in the world at their conferences and institutions. Her 2014 book, The Origin of Life Circus, contains eye-opening interviews with the biggest authorities. All of them disown the well-known “RNA World” scenario, at least in its original formulation, despite its continuing presence in the media. Some think RNA had a role in combination with other molecules like proteins. But relying on proteins and other molecules undermines the whole reason for the RNA World, to try to account for metabolism and genetics in one molecule. Steven Benner, for instance, lists four paradoxes of RNA: (1) the building blocks tend to form tar, (2) RNA can’t form in water, (3) RNA polymerization goes against thermodynamics, (4) ribozymes are more likely to destroy RNA than build it (pp. 155-156). The bottom line is that RNA could not have worked alone. It needed proteins as helpers, as well as a container or membrane to hold everything together.The problem with proteins and polynucleotides is getting the sequence right. Even if they could join up easily (which they don’t), unless they can actually do something, they cannot be building blocks to a living organism. As many have pointed out (including our online book), the probability of getting functional sequences under ideal conditions is infinitesimally small. If one usable protein would never form on Earth in the entire history of the universe, how much less 473 proteins in Venter’s minimal living cell? Each person interviewed in Mazur’s book sang the same refrain: we have no idea how life arose.Materialists, come to your senses. It’s hard to kick against the goads. The reality of life is telling you something. It’s shouting. Why resist any longer? You respect evidence, don’t you? Faith in the impossible runs against your values. Follow the evidence where it leads. It’s the scientific thing to do. (Visited 118 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

Photo library: Business and industry 1

first_img{loadposition tc}Click on a thumbnail for a low-resolution image, or right-click on the link below it to download a high-resolution copy of the image.» Download Business & Industry contact sheet (1.8MB) » Download full image library contact sheet (10.5MB) Johannesburg, Gauteng province: A bird’s-eye view of the Absa Bank call centre in Auckland Park, where about 1 800 staff provide telephonic support services.Photo: Chris Kirchhoff,MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: A bird’s-eye view of the Absa Bank call centre in Auckland Park, where about 1 800 staff provide telephonic support services.Photo: Chris Kirchhoff,MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: A bird’s-eye view of the Absa Bank call centre in Auckland Park, where about 1 800 staff provide telephonic support services.Photo: Chris Kirchhoff,MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: Jabulani Mall, one of the many new shopping centres being constructed in the city’s townships as a result of the country’s rapid economic growth. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: Jabulani Mall, one of the many new shopping centres being constructed in the city’s townships as a result of the country’s rapid economic growth. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: Naledi Mall, one of the many new shopping centres being constructed in the city’s townships as a result of the country’s rapid economic growth. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: The recently opened Maponya Mall, the flagship of Soweto tycoon Richard Maponya’s many enterprises. Constructed at a cost of R650 million (some US$100 million), it is the third, and now largest, shopping centre in the township. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: The recently opened Maponya Mall, the flagship of Soweto tycoon Richard Maponya’s many enterprises. Constructed at a cost of R650 million (some US$100 million), it is the third, and now largest, shopping centre in the township. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res image Johannesburg, Gauteng province: The recently opened Maponya Mall, the flagship of Soweto tycoon Richard Maponya’s many enterprises. Constructed at a cost of R650 million (some US$100 million), it is the third, and now largest, shopping centre in the township. Photo: Chris Kirchhoff, MediaClubSouthAfrica.com » Download high-res imageBUSINESS AND INDUSTRY 1: {loadposition business}Having trouble downloading high-resolution images? Queries about using the image library? Email Mary Alexander at [email protected]last_img read more

A new Lake Erie battle: Lucas County sues U.S. EPA over western basin water quality

first_imgShare Facebook Twitter Google + LinkedIn Pinterest By Peggy Kirk Hall, director of agricultural law, Ohio State University Agricultural and Resource Law ProgramDisagreements over how to improve the health of Lake Erie have led to yet another federal lawsuit in Ohio. This time the plaintiff is the Board of Lucas County Commissioners, who filed a lawsuit in federal court in April against the U.S. EPA. The lawsuit accuses the U.S. EPA of failing to enforce the federal Clean Water Act, which the county believes has led to an “alarming” decline in the water quality of western Lake Erie.The Clean Water Act requires states to monitor and evaluate water quality and establish water quality criteria, and also to designate a water body as “impaired” if it does not meet the criteria. Once a water body is on the impaired waters list, the state must create Total Maximum Daily Loads (TMDLs) for the water body. TMDLs determine the maximum amounts of each pollutant that can enter a water body and still allow the water to meet the established water quality criteria. Plans for reducing a pollutant would be necessary if the pollutant exceeds the TMDLs. The state’s efforts to establish the water quality criteria, designate impaired waters and develop TMDLs are subject to review and approval by the U.S. EPA, who must ensure that the states are taking adequate action pursuant to the Clean Water Act.Lucas County alleges that the U.S. EPA has failed in its Clean Water Act obligations by allowing Ohio to refuse to prepare TMDLs for the western basin of Lake Erie. Even after another court battle forced the designation of the western basin as “impaired,” the county explains, Ohio’s EPA declared the western basin to be a low priority for TMDL development and has not yet proposed either TMDLs or an alternative plan for addressing the basin’s impaired water status. Lucas County argues that since Ohio has not established TMDLs for the impaired waters of Lake Erie, the U.S. EPA must step in and do so.The county also contends that the lack of state and federal action on the impaired waters status of the western basin has forced Lucas County to expend significant resources to maintain and monitor Lake Erie water quality for its residents. According to Lucas County, such actions and costs would be unnecessary or substantially reduced if the U.S. EPA had fulfilled its legal obligations to ensure the preparation of TMDLs for the western basin.Agricultural pollution is an explicit concern in the county’s complaint. The development of TMDLs for the western basin would focus needed attention and remedial measures on pollution from agricultural operations, Lucas County states. The county asserts that TMDLs would establish a phosphorous cap for the western basin and methods of ensuring compliance with the cap, which would in turn address the harm and costs of continued harmful algal bloom problems in Lake Erie.The remedy Lucas County requests is for the federal court to order the U.S. EPA to either prepare or order the Ohio EPA to prepare TMDLs for all harmful nutrients in the western basin, including phosphorous. The county also asks the court to retain its jurisdiction over the case for continued monitoring to ensure the establishment of an effective basin-wide TMDL.This is not the first TMDL lawsuit over the western basin. In early February of this year, the Environmental Law and Policy Center (ELPC) and the Toledo-based Advocates for a Clean Lake Erie filed a lawsuit that similarly alleges that the U.S. EPA has failed to require Ohio to establish TMDLs for the western basin, which is still ongoing. The case followed an earlier and successful push by the ELPC to order Ohio to declare the western basin as impaired, which the state had refused to do previously.The newest round of litigation again highlights differences in opinion on how to remedy Lake Erie’s phosphorous pollution problem. Like the TMDL lawsuits, a successful effort by the Toledoans for Safe Water to enact the Lake Erie Bill of Rights was also predicated on claims that Ohio and the federal government aren’t taking sufficient action to protect Lake Erie. Lucas County made it clear that it isn’t satisfied with the state of Ohio’s approach of providing funding to promote voluntary practices by farmers to reduce phosphorous pollution, despite stating that the county isn’t “declaring war on agriculture.”In its press conference announcing the current lawsuit, the county explained that the state’s voluntary approach won’t provide the “sweeping reforms we need.” On the other hand, the Ohio Farm Bureau has argued that the TMDL process for Lake Erie can take years longer and be less comprehensive than the voluntary practices farmers are pursuing. Still others believe that more research will help us fully understand the phosphorous problem and identify solutions.As battles continue over the best approach to improving Lake Erie’s water quality, maybe all could at least agree that litigation is costly, in many ways. An alternative but perhaps more challenging path would be appreciation of the concerns on both sides of the issue and cultivation of collaborative solutions. Let’s hope we can find that path.last_img read more

Data Access up in the Air

first_imgTwo announcements over the last couple of days stand in an interesting contrast to each other.  One is Google’s announcement of Google WiFi and the availability of free WiFi access across all of the city of Mountain View.  The second is Boeing’s announcement to exit from providing WiFi access on board carriers flying Boeing aircraft in December 2006, after having equipped 156 aircraft with their Connexion service, including those from carriers like Lufthansa, SAS and Singapore Airlines. (This follows an announcement in June of Verizon to also exit the in-flight phone business.)Access to things like VoIP, web-based on-line services and data content, like that of our own Formtek | Orion repository, or any of hundreds of other kinds of services from anywhere and anyplace is enticing.  The net is becoming (or has become) the driving force for business communication and data.  Google’s roll-out across the entire city of Mountain View seems to have been challenging and have had a few glitches.  All transmitters are not in place just yet either.  Also the disclaimer that the service is an “outdoor service” and does not work well in-doors is a bit disappointing.  Considering the service has only been up a few days, it seems to be doing well — I’m looking forward to the planned roll-out in San Francisco.The exit of Boeing and Verizon from in-flight WiFi might prove to be an interesting alternative for Google.  For example, immediately after Boeing’s announcement ASiQ in turn announced that they see Boeing’s exit as greater opportunity for them.  Boeing’s Connexion was based on technology circa 2000.  It’s only six years, but technology has changed quickly and ASiQ has developed a much cheaper alternative. There has been a lot of press about Google’s efforts to try to penetrate the Enterprise market.  While free community-wide net access is great (especially if it is somewhere that I’ll be frequently), I wonder that if Google is really serious about the Enterprise that it might be a better and more cost-effective strategy for them to provide free WiFi in places like airports and airplanes, places where business people are in high numbers.  It seems like it would be far easier and have fewer obstacles in getting approval to do something like that rather than to try to blanket the landscape of an entire community with WiFi.last_img read more