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  1. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    umm, yeast artificial chromosomes have been around for decades That is how insulin is manufactured. People HAVE published similar findings in the early 80's.

    The reason it wasn't published recently is not that it wasn't submitted for publication but rather the journals REFUSED to publish it because it wasn't novel.

  2. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    I challenge you to point out anything in my original post that is inaccurate.

    The only novel chemicals they synthesized were the sugars. The bases were already commercially available.

    PCR is NOT amplified blindly. You provide two short sequences pointed in opposite directions. The DNA polymerase enzyme requires these to attach to the DNA molecule and begin transcription. If you try to use PCR to amplify everything, you will get nothing at all. The polymerase will not be able to function. You obviously don't know how this process works. This is a fundamental requirement of PCR. In order to amplify everything you must clone it in sections into bacteria and grow the bacteria. This is why the human genome project took so long.

    DNA fingerprinting is NOT a random process. First you amplify specific section of for sample DNA using PCR, typically with a marker on the added during the PCR. From these amplified sections you then use DNA nuclease's like EcoR1 and others to look for uniques point mutations. This is done for several reasons. First, there is too much DNA in a human cell to get anything but an indecipherable smear if you try to use it all. Next, most samples don't have nearly enough DNA to visualize effectively without amplification. Finally, PCR is an elegant way to incorporate either a radioactive or fluorescent marker. Again, the fact that it is NOT a random process is what makes this test usefully. I am fairly certain that CSI has talked about this. Therefore I can only assume that you haven't every researched this technology and that you don't like cop shows.

    In the 70's when PCR was invented you are correct, creating short sequences was annoying but not difficult. First you began with a single nucleotide attached to a surface. You then added blunted nucleotides to your dish. This would react with your attached nucleotide forming a 2 nucleotide chain. You then was off the extra. Next you add an enzyme to activate the just added nucleotide by attaching a phosphate group. You repeat the last two steps with various nucleotides to build up your sequence. When you are done you detach the chain from the surface and purify it. Annoying, time consuming but not difficult. Since about 1983 you could purchase custom sequences from catalogs. The protocol is very conducive to robotic synthesis. I have personally ordered sequences of 100+ base pairs and could have easily ordered several thousand base pairs. Again you demonstrate your lack of knowledge of the actual state of technology.

    People have been creating custom DNA molecules like were described in this article for 20 years.

    My complaint is not that this isn't interesting but rather that it doesn't deserve publication. They did nothing novel and therefore it shouldn't have been published in a peer review journal.

  3. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    Not on me but it has been 10 years.

    We used them to create random point mutations in a gene sequence which we then cloned into bacteria.

    But I would like to mention that AZT, the first AIDS drug, is just a non-standard nucleotide which happens to mess up the RNA reverse transcriptase enzyme. People have been popping pills of this papers "novel" nucleotides for 20 years.

  4. Re:Can they use silicon in place of Carbon? on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    I very much agree with you with one exception:

    2) but it's apparently *really* difficult to get life started.

    we don't have the telescope resolution to really see if life exists elsewhere. We can't see earth sized planets and we can't analyze the atmosphere of the ones we do see. Life COULD exist there and we wouldn't know it.

    All we can say is that intelligent life at the industrial age or better (which is when we could have a chance of detecting them) is non-ubiquitous.

  5. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 2, Insightful

    My objection is not that this isn't "neat." I am always looking out for stuff like this.

    My objection is that it was published in a peer-reviewed journal! This type of article deserves to be on the discovery channel or scientific American magazine, NOT in a legitamet scientific journal.

    If the artuicle had been about building nanostructures and they had to develop this process to do it that is one thing. But this is the equivalent of saying "I have one rock stacked on another...this may or may not be usefull to build a house." While the technology is different, the end result does not deserve publication any more than my stacked rocks.

  6. Re:Can they use silicon in place of Carbon? on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    Life really isn't possible for anything but Carbon or Silicon. The reason I can say that is the number of bonds. 4 bonds allow for extensive and complex networks which complex chemistry requiers. Boron, tin, lead etc can't do this.

    We essentially live on a planet with an over abundence of silicon and a virtual absence of carbon. Silicon is so much more plentiful than carbon it is almost silly. On proto-earth the only availible carbon source was the atmosphere and in a water world, like earth, air is a lousy place to get your food.

    Silicon COULD be used in life but is very unlikley to arrise spontaneously. We could design life to use silicon in theory.

  7. Re:Can they use silicon in place of Carbon? on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    However on further though let me add that while I don't think life would EVER spontaneously arise using silicon, it would be theoretically possible to artificially create a silicon based life.

  8. Re:Can they use silicon in place of Carbon? on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 3, Interesting

    Yes...I am still convinced that carbon would rule the roost.

    In order for silicon to even remotely compete, Silicon dioxide would have to be gaseous. At the several hundred degree higher temp, large and complex molecules become unstable.

    In addition silicon is a larger atom which creates a greater limit on structures than carbon.

    Carbon would still be used with Ammonia. Using methane absolutely requires carbon (methane being a hydrocarbon).

    There is no known condition in which silicon would be preferable while still allowing for large complex molecules.

    I get annoyed when people ignore basic physics and chemistry for their own pet beliefs.

  9. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 0, Troll

    Thanks for the link...I will read it thoughly in the next day or two.

    As for me being "worked up." I am annoyed that this sort of "research" is published when it doen't add anything to general knowledge. It may turn out that novel bases are usefull. However this paper is not since they are just demonstrating that you can make DNA with alternate bases...something that is known for a long time.

  10. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 3, Interesting

    First: C-Nucleosides are nothing new and are readily availible in catalogues

    Second: Life already uses a wide variety of non-coding nucleotides typically created through post synthesis modification. One example of post synthesis modification used to control coding is methylation.

    Unfortunetly, Slashdot lack of imagination and narrowmindedness when it comes to anything has lead to an automatic acceptance of everything as "neat." This is an example of wasted research money that did not creat new information and has not lead to any new insights into nature.

  11. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 2, Interesting

    I work in pharmaceuticals. I am constantly shocked by what random chemicals someone has in stock just sitting there.

    Just because you can't buy them from a drug store doesn't mean it isn't readily availible (for the right price)

  12. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1

    Hmm, I can't see any negative mod points on any of thoes posts and new modding doesn't change the history.

    I bet thoes people have poor Karma and so they aren't given free points when they post.

    As for designing complementary nucleotides, yes that is slightly more difficult....However I had the capability of doing it 10 years ago with a piece of chemistry modeling software that requiered for every freshman at my school. After you have complementary chimicals you could probably just order them from a catalogue and even if you couldn't you could synthesiae them yourself rather easily.

  13. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 0, Troll

    I am willing to bet that it is a "Letter to the Journal" or some other non peer reviewed section.

  14. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 3, Interesting

    Actually, I made a living for a number of years doing research with PCR.

    I sited DNA fingerprinting because it is a process that most people have heard of that uses PCR. Notice I said it was an example. My post was intended for those people WITHOUT advanced degrees in Biology/Chemistry. If you would like to talk about annealing temperatures, extension times, point mutations, hair-pin turns or anything else let me know.

    You are also right, DNA is not just sugar. It also includes the base and the phosphate group. However my snide remark is still valid. You are not talking about unusual chemistry. I am willing to bet good money that every component was readily available already.

    This team did nothing novel. As you pointed out, there are automated processes to manufacture short chain nucleotide chains. These machines are already capable of including single point mutations of non-typical nucleotides. All they did is fill up the machine with there off the shelf chemicals and hit go. They then re-ran the program but in reverse. When they mixed the two batches together....DNA molecules!

  15. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 4, Interesting

    Ummm...that alternate nucleotides were possible was proven 30 years ago. Synthetic DNA was only created 20 years ago.

    While the 4 bases used do have some advantages in sysntesis, stability and other effects, tehre is no compelling reason that requiers thoes 4 bases.

    I have no idea how this got published...The reason a similar article hadn't been published earlier is because every reputable scientist in the field agrees with you:

    Now, I don't really see any immediately obvious applications for this new molecule

    This article did nothing to expand our knowledge. It didn't prove anything. All it showed is that the machine they ALREADY had in the lab could do everything the manual they got with it said it could.

    BTW, I don't see any responses modded down like you suggested...

  16. Re:Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1, Informative

    Yes, it's been done for 20 years.

    Using alternate nucleotidtes is a usefull way of creating random mutations during PCR. I have personally used these in some lab experiments in college.

    It IS true that there is no record of anyone creating a stretch of DNA with exclusivly alternate bases. This is not because of a technical limitation but because there is no practicle use for doing it.

  17. Re:Can they use silicon in place of Carbon? on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 3, Informative

    They can...but you wouldn't want to.

    Silicon also has 4 bond sites which you need for the complex chemistry of life. You can make identical molecules except switch silicone for carbon.

    But life will almost certainly NOT do this elsewhere.

    Silicon chemistry takes more energy than carbon chemistry.

    As an example I will point to earth. Silicone is hundreds of times more common than carbon in the crust yet life did not evolve to use Silicone, it instead used the less common carbon.

  18. Whoopee! on First DNA Molecule Constructed from Mostly Synthetic Components · · Score: 1, Interesting

    So in other words we can synthesize a variety of sugars.

    We can then take these sugars and string them together.

    Just for reference, custom oligo DNA chains have been available for purchase for the last 20 years. This is what makes PCR (DNA fingerprinting for example) work.

    I call "pointless" on this demonstration.

  19. Re:The moon does a lot of different things... on Mars Had an Ancient Impact Like Earth · · Score: 1

    The accurately explains the content of the atmosphere, 95% CO2 and a mix of others. It does NOT explain why Venus has 100 times the atmosphere for a nearly identical planet.

    All the calculations suggest that Earth's atmosphere SHOULD be much thicker than it is. The reason it isn't is because much of the proto-Earth atmosphere was blown away during the impact and the moon, especially early on when it was much closer, provided enough tidal effect on the atmosphere to let some of it escape thus reducing the overall amount of atmosphere.

  20. Re:The moon does a lot of different things... on Mars Had an Ancient Impact Like Earth · · Score: 3, Informative

    Tidally locked means that one face (the denser one) of the satellite always faces the parent. Currently the moon is locked to the earth. In time the earth MAY lock on the moon but that is unlikely because the moon's orbit is gradually expanding (due to tides) and the effect is gradually decreasing. But I don't believe there is an example of a parent tidally locking on a satellite (Pluto and Charon are essentially orbiting each other therefore both are parents)

    When compared to literally every other satellite system in the solar system except for Pluto-Charon, the moon is a gigantic proportion of the earth's mass. The primary protection from locking on the sun is because the mass distribution shifts. Therefore there isn't one "face" of the earth-moon system that is denser all the time.

    The primary source for #3 and 4 is venus. Venus is almost the identical size. While venus has higher solar flux that doesn't explain the dramatically thicker atmosphere, lack of plate tectonics and much colder core. The moon is the only other difference. So it is either the large satellite or the impact that cased the differences.

    #5 and 6 are related. We know that the moon is significantly less dense than earth. We know that the earth is denser than venus even though they should be almost identical. We know that the earth and moon have essentially identical isotope ratios. Since the moon is less dense it's radius is large in ratio to earths which creates a shield that blocked up to 20% of the impacts earth would have experienced. Since the earth has a over large percent of metals, they WOULD get distributed throughout the planet. Mostly to the core but also to the mantel and crust. Since it is higher than expected, the amount of metal in the crust is higher than expected. Metals are vitally important to life. Since the moon is metal poor and that the similar isotope ratios prove that the earth and moon are formed from the same mix, it is only reasonable to assume that the higher metal content came from the impact that created the moon.

  21. Re:The moon does a lot of different things... on Mars Had an Ancient Impact Like Earth · · Score: 1

    Current numbers say that the core should be Significantly cooler than it is even considering radioactive decay. Venus, almost the identical size as earth has not tectonic plates and it's core is approaching solid. The only difference is the moon. The moon causes the earth's crust to warp which generates heat. This is the same thing that Jupiter does to Io but on a much smaller scale. The internal (thermal) convection followed by slab pull is powered by the tides caused by the moon.

    As for #6. Yes both Earth and Theia already had cores. When it hit it was not a direct blow but an of center one. The impact pulverized Theias crust and blasted a large portion of the earth's crust into orbit which eventually formed the moon (and some theories say that the pacific ocean is the scar of this impact). The core of Theia sank and eventually merged with Earth's creating a larger core than would be expected (the same thing happened to Mercury which is why it is so dense). As Theia's core sank it churned up the mantel mixing a very high level of metals into the mantel and crust. After they merged they larger core provided a larger metal source which leaks cycles through the mantel and makes it into the crust which artificially raises the ratio of metals. Appollo trip have shown that while the isotope concentrations prove that the earth and moon have the same source, the proportion of elements, especcially heavy elements is very different. This is why the moon is less dense than the earth.

    Because the moon is less dense than the earth it's radius is a large portion of earth's. This forms a sort of shield which blocked something like 20+ percent of impacts early on and still block a significant fraction of impacts. In addition since very few impacts are caused by random orbits but are instead caused by objects in similar orbits to earth, it is much more likely that the moon the have a chance to block them before they hit earth

  22. Re:Where's the ejecta? on Mars Had an Ancient Impact Like Earth · · Score: 2, Informative

    Depending on how it hit the debris may have been put into a retrograde orbit which is less stable.

    Mars is significantly smaller so it is not able to hold onto it's satalites as easily...it could have escaped.

    The collision is smaller than the earth-moon collision. There may have been less matter kicked up.

    If it was very glancing then any debris would have more than escape velocity anyway...

  23. Re:The moon does a lot of different things... on Mars Had an Ancient Impact Like Earth · · Score: 3, Informative

    Actually, the moon, by displacing a large portion of the mass, has prevented the earth from being as tidally locked to the sun as it should be.

    Since the earth-moon system presents a profile to the sun that is constantly changing, the sun's gravity can't tidally lock the planet. Mercury is tidally locked. Venus almost is. Without the moon we would have have a day length of several months. Notice how Mars has a day a little longer than ours and Jupiter is at 15 hours for a day.

    What you are thinking about is the tidal friction between the earth and moon. Yes, this ALSO slows down the earths rotation but it is a much slower process and provides benefits which I outlined in my prior post, namely plate tectonics and a molten interior.

    Tell me, what else do you think is incorrect?

  24. The moon does a lot of different things... on Mars Had an Ancient Impact Like Earth · · Score: 4, Informative

    There are several things that our extremely large moon does for us that make life much more comfortable.

    #1 is of course tides that are more extreme than the sun could generate

    #2 rotational speed. The moon has kept our rotation from slowing as much as it should have. Shorter day/night cycles are important for environmental management.

    #3 atmosphere. The moon helped reduce the density of proto-earth's atmosphere. Without it we probably would resemble Venus.

    #4 plate tectonics. The tidal influence on the crust heats up the mantel and keeps the plates from sealing

    #5 protection. The moon intercepts a large percentage of the impacts destined for earth. This reduces the disruptions caused my meteor impacts. This was more pronounced earlier, when the moon was closer and when it was even more important (more meteors around)

    #6 increased metal content. Since the moon is almost entirely light minerals, most of the metals that were in the original impact were left on earth which artificially increased the concentration of metal in the crust.

    While I can think of other things that could help with one or two of these, I can't think of something that would satisfy all of these consistently for a few billion years.

    What do you suggest as an alternative?

  25. I am more concerned about the distance... on Higher Oil Prices Are Starting To Bring Jobs Home · · Score: 2, Interesting

    from my home to my office....when will my company start teleworking as an option!

    But US jobs and stable prices despite the raising fuel costs is great news!