http://abcnews.go.com/blogs/technolo...lanet-in-past/

Mars rover finds proof life could have thrived on the planet.

Discoveries Suggest Icy Cosmic Start for Amino Acids and DNA Ingredients
 

Astronomers have detected the building blocks of DNA in an interstellar gas cloud located about 25,000 light years from Earth.



https://fbcdn-sphotos-g-a.akamaihd.n...72667091_n.jpg


http://www.nrao.edu/pr/2013/newchem/

Breaking Science News
 

"Scientists working with data from a large particle accelerator in Europe are now almost certain they have pinned down the elusive sub-atomic particle known as the Higgs Boson," NPR's Joe Palca tells our Newscast Desk.

http://www.npr.org/blogs/thetwo-way/...paign=20130314

http://i1277.photobucket.com/albums/...psfffb1b27.jpg

Voyager 1 at the absolute limit of the solar system
 

So the Voyager 1 probe has reached the absolute outer edge of Sol's influence. Earlier today it was announced that Voyager 1 had left the solar system and had now entered interstellar space but that might be a bit premature. There are still charged particles from the Sun being detected but when the direction of those charged particles change (meaning that they are inbound to the system and not outbound from it) then the probe will truly be in interstellar space.

How far is Voyager 1 from Earth? It is 72 light hours. That means it takes a radio signal, which is just a form of light, 72 hours to travel from the spacecraft to Earth. Light travels at 186,282 miles per second. That's 670,615,200 miles per hour so 48,284,294,400 miles away. Purely for sake of comparison the Moon is 1.5 light seconds away (~250,000 miles) and the Sun is 8 light minutes away (93 million miles).

This is now the farthest out anything made by the hands of humanity has ever been from Earth.

Cheers
Aj

I heard a story the other day on NPR in which they were discussing a book titled Frankencat, about some of the different genetic modifications that are being performed on animals. Specifically, the story was about how spider DNA has been introduced into goats so that when the goat's milk is purified, it contains a significant amount of silk that can be harvested and used in any number of applications. Because silk is super light but very strong, it's being looked at for use in things like bullet proof vests, etc.

I had to google to get the right book.
http://www.npr.org/books/titles/1735...ave-new-beasts

Oh, ha, oops! I was in the car and no doubt yelling at some dumb ass who was driving poorly. Thanks for finding that. I think at one point the commentator said "Frankencat" and it stuck in my mind.

Such a great class...
 

This reminds me of when I took Molecular Genetics in college. The scientist who taught discussed how their exists a fish whose blood contains a distinct "anti-freeze" gene. (I'm unclear how it is used originally by the fish.) This anti-freeze gene has since been isolated from the fish, reproduced in a laboratory and ultimately transferred into the genome of a strawberry. The idea was to prevent strawberry crop loss from untimely freezing etc. I'm sure there are people who scoff and otherwise flip out about this but honestly, I think that shit is bitchin' !

This was being discussed when I worked at Whole Foods, specifically introducing cod DNA into tomatoes to make them impervious to cold and what the ramifications would be for people who, for example, adhere to a vegan diet.

http://news.yahoo.com/ancient-egypti...180758166.html

On a lighter note, oldest yet sundial found

The gene is in a fish that, if memory serves, lives under one of the ice packs either the Arctic or the Antarctic. It literally evolved a means of keeping its blood from freezing. Like you, I think that it is so amazing and I really wish there were some way to communicate so that the general public would understand that there's no 'essence of fish' that is taken out and put it into a strawberry. Rather, a specific gene that builds a very particular protein, is inserted in another organism which then can build that protein. It's the same protein. It does the same thing. A gene that codes 'for' something codes for that thing not all of the traits of the organism the sequence came from. All living things can transcribe the same DNA because the bases ACGT are the same in fish and in plants and in mammals. It is a sign of the unity of all life on this planet that the gene that says "build eyes here" is the same in the fruit fly, mice and humans.

The fact that the gene originally came from a fish wouldn't trigger a fish allergy because the DNA in the strawberry doesn't 'know' that it came from a fish. It knows that when it gets a signal to start making some protein X, it starts making that protein until some other signal tells it to stop.

Cheers
Aj

But Hollylane, that strawberry isn't in its natural state. Everything we eat, every fruit and every vegetable and every domesticated animal has been genetically modified. The difference between genetic engineering and what humans have been doing since we invented agriculture is two-fold:
1) Instead of doing things blindly we are being far more targeted and subtle with it.
2) We are able to across the species barrier in ways we couldn't before.

Other than that, the essence of what is happening is exactly the same. We are taking genes and selecting the ones we want/need for our purposes. When I say we are no longer doing things blindly I mean that in the past, all we could do was take one plant or animal that had traits we wanted and cross it with another planet or animal that had traits we wanted. The problem was that many traits don't breed 'true' and there could be genes that were 'hangers on' that might bring in traits we didn't want.

Now, if we want to breed for a particular trait, all we have to do is know what genes or combination of genes code for the appropriate protein.

The second issue, being able to cross the species barrier, I can understand a bit more but it still seems, to me, to rest on an essentialist view of living things. Even you say so below that you want a strawberry to only be a strawberry as if the insertion of a gene that makes a protein that prevents damage from freezing somehow makes it not a strawberry. The *only* reason why strawberries never hit on this neat little trick is that Nature never put that species in the position where the ability to resist extended cold was selected for. Plants have a different mechanism for surviving cold and, in the case of strawberries, it's called 'seeds'. But if strawberries had evolved in an environment where it was *always* cold (like under the ice pack) then they almost certainly would have hit on a similar trick. We are not, however, taking some essence of fish and putting it into a strawberry. We're simply taking a gene that, for reasons of historical contingency and evolutionary history, found itself in a fish and putting it in a strawberry where it does the same thing as it does in the fish. Nothing 'fishy' comes over because the protein *happens* to come from a fish, it isn't necessarily a protein that a fish and only a fish could ever have need of.

So why didn't the strawberry come up with anti-freeze on its own? Here I have to digress into evolutionary biology because it's the only way to make sense. I'm going to use two examples to explain evolutionary contingency, one real and one fanciful.

First the real:

The primate eye is actually built 'upside down'. What one would expect, if the eye had been designed by, say, an optical engineer that the light-sensing cells would be facing the source of light with all of the supporting infrastructure (blood vessels, etc.) behind the eye. That is not, in fact, how the primate eye is built. Instead, the light sensing cells are at the *back* of the eye and all the other structure of the eye is on top of it. This means that our eyes are less efficient then they otherwise could be. Now, if evolution could take steps backward the primate eye could have been rebuilt over evolutionary time so that it was more efficient (the eyes of cephalopods--squids and the like) are actually built the right way round. But evolution can't take back steps it can *only* work with what it already has.

The other example is the potential for human flight. The reason why we *can't* fly isn't that it is impossible for us to develop wings but that all of the things it would take for us to develop wings are simply not available to our species. Those pathways were closed off millions of years ago and there's no way to go back even though the ability to fly like bats would be mightily helpful to our species. Strawberries and fish haven't shared a common ancestor for hundreds of millions of years. The reason why the fish and the strawberry would never meet isn't that nature doesn't *want* them to but because there's no pathway by which they *could* meet. Not because there's something 'wrong' with it but simply because there's no selective benefit for either the fish or the strawberry to trade genes with one another.

Lastly, there's the issue of commonality of genes. While you look nothing like a banana you share 70% of all your genes with bananas. You are also not much like a fruit fly or a mouse (although you are, obviously, much more closely related to a mouse than a fruit fly) yet the very same gene that tells the developing human body "build eyes here" tells both the developing mouse or fruit fly to "build eyes here". To think about the implications of this try this thought experiment. If we took the gene, called 'eyeless', out of a human being and implanted it in a mouse what kind of eye do you think would grow? If you said "a human eyeball" you're wrong. It doesn't. The gene doesn't specify "grow this kind of eyeball here" instead it specifies "whatever kind of eye is appropriate for this species, it goes here". Do we know this to be true? Yes. How? Because we can and have taken that gene from a fruit fly, inserted it into the genome of a mouse where that gene had been 'knocked out' and pasted it in. Mice grew mice eyes where the gene specified it should. The same thing worked in reverse. A copy of the eyeless gene from a mouse, inserted into a fruit fly, caused the fruit-fly to grow a fruit-fly eye in the specified location.

Was there anything 'mouse-like' about the gene? No. In fact, there's a gene--the HOX gene--that specifies the body plan for almost everything living on the planet that *isn't* a bacteria.

DNA is DNA. There's no such thing as 'fish' DNA which is different from and incompatible with banana DNA. DNA either codes for a protein or tells another strand to start or stop.

I'm not saying we should go full-speed ahead with genetic engineering but I am saying that there is a lot of confusion and, in my mind, needless fear of the technology. I am not, let me be clear, defending Monsanto or any other agribusiness. I am talking solely about the scientific questions of genetic engineering.

At the end of the day, selective breeding and genetic engineering are the same kind of thing. Selective breeding is walking, genetic engineering is ballet.

Cheers
Aj

Thanks for the response. Can I ask you a couple of follow-up questions?

1) Since you agree that a protein is just a protein, why does it matter where it came from? I mean I could understand if the protein were, say, one that causes persons with an allergy to peanuts to have a reaction but provided its *not* one that causes an allergic reaction why does it matter?

2) What do you mean by maybe the pathways don't exist in nature for a multitude of reasons?

This is the deeper question, to me, and the reason I'm a little confused about it is this; it seems to me that the explanation I gave, just to take one for instance, why strawberries never developed anti-freeze on their own is sufficient to explain why that genetic pathway had to wait until we came along to show up in that species. For example, it would be extremely useful if humans could see down into the infrared and up into the ultraviolet. We *know* it's possible because there are other animals that can see into either one but our genome was simply never faced with the correct set of problems that would push us toward being able to do so. It's not that there's some grand design nor is it that there's something *wrong* with being able to see a little farther along the EMF spectrum than we already do, rather it's that not only Homo sapiens but primates as a whole were never in any environment where the selection pressure pushed *any* of us toward being able to see into the IR or the UV parts.

That explanation is sufficient to explain why we can't see UV or IR and there doesn't need to be any other reason. Likewise, the fact that strawberries--because they are flowering plants--never had the problem of "what do you do when your entire life-cycle is spent underneath an ice pack" is sufficient to explain why they never developed anti-freeze. Since strawberries are native to latitudes where winter is, more or less, what those of us living in the temperate zones are used to the long-standing plant solution toward the cold (e.g. produce seeds which can spend the winter underground) and that has been sufficient to preserve strawberry genes down the ages. No other explanation is really required. Why go to the trouble of evolving anti-freeze when the cold that could kill you is only 90 days long and you can just keep your genes in a seed for that period of time? No reason. Just like primates came up with a pretty decent solution for not being able to see well in the darkness--don't be active at night. Hominids came up with an even more elegant solution--fire.

I'm asking these questions of you not because I'm trying to prove some point but because most of the time when I've engaged others in this topic they haven't understood the science and so they've had some rather profound misconceptions about the nature of genes, the nature of proteins, the nature of DNA or they haven't really grasped that, for instance, while fruits *want* to be eaten vegetables, on the whole, *don't*. (I'm speaking metaphorically, of course, neither fruits nor vegetables 'want' anything.) So what is the problem with genetic engineering, in general? Not Monsanto's business practices (that's a separate issue) but with genetic engineering specifically?

Why is it unnatural to take a gene that does precisely what we want done and *only* that thing and implant it in a species unnatural when if we simply selectively bred for resistance to cold and got to, more or less, the same protein but it took us a thousand generations (plant not human) to get there it would be natural? It's the same protein, it does the same thing, the only difference is one is a one-step process and the other is a blind, multi-step process with each step along the way having a risk of picking up genes we don't want and which might have deleterious effects.

Thanks for answering. It's a rare treat to be able to ask someone who understands the biology, can do "gene's eye view" thinking, grasps the 'central dogma' of modern molecular biology (that genes code for proteins) and still is opposed to genetic engineering in the terms you've expressed above.

Cheers
Aj

New kind of supernova discovered
 

http://www.huffingtonpost.com/2013/0...n_2957362.html

There's a new kind of supernova that's been discovered this one when a white dwarf explodes (which, honestly, I didn't think they had the mass to do).

Also there's a storm on Venus that has been going on for six years. That's nothing compared to the hurricane that is the Great Red Spot on Jupiter. That storm has been going on since at least the 1600s when Cassini first observed it.

http://www.huffingtonpost.com/2013/0...tml?ref=topbar

It's quite something to think about a storm that's been raging for centuries. I wonder what causes something to become classified as a storm vs. simply being considered an atmospheric condition. Is it that it's different than on most of the rest of the planet?

Depends on why that person is vegan. If it's for health reasons (which I am led to believe is a very common reason), unless the DNA changes the nutritional content of the tomato in some non-negligible way, it should be completely irrelevant. If it's for reasons of not wanting to harvest sentient life (read: things with a nervous system/motivational system/ability to feel pain/etc.) as a food source, then unless this DNA gives the tomatoes a bloody nervous system or live fish have to be continuously slaughtered for a source of the DNA (depending upon how the original DNA must be obtained this might be the case until you have a seed population of the modified tomato to work with, but after that, you can probably just have the tomatoes reproduce), it should not be particularly relevant.

Now if it's for reasons of religion or spirituality, or just Luddism or thinking there's some kind of magical essence of fish or whatever, I got nuthin'.

PS, slightly related: I am totally looking forward to vat-grown meat one of these days. Meat that does not require the continual harvesting of sentient animals to obtain. Bacon has already been produced from pig stem cells, which is pretty awesome. Now I'm just waiting for the day the tech advances to the point that we can find meat in the supermarket labeled "NO ANIMALS WERE HARMED IN THE MAKING OF THIS MEAT." The culture shock alone will be priceless.

I don't think there's anything inherently bad with GMO, to be honest. I expect this will be a very unpopular opinion but, it's mine.

I think the implications for vegans is an interesting one though-

Are you talking about Colony Collapse Disorder?

If so, here's some data from the EPA website:
Why it's happening
There have been many theories about the cause of CCD, but the researchers who are leading the effort to find out why are now focused on these factors:

increased losses due to the invasive varroa mite (a pest of honeybees);
new or emerging diseases such as Israeli Acute Paralysis virus and the gut parasite Nosema;
pesticide poisoning through exposure to pesticides applied to crops or for in-hive insect or mite control;
bee management stress;
foraging habitat modification
inadequate forage/poor nutrition and
potential immune-suppressing stress on bees caused by one or a combination of factors identified above.

Additional factors may include poor nutrition, drought, and migratory stress brought about by the increased need to move bee colonies long distances to provide pollination services.


I think when making broad and sweeping declarative statements, it's most helpful to offer a scientific citation. The best information being the most accurate and thus by definition, evidence based.

Yes. This exactly. Thanks for the reference!--pretty amazing stuff!
(I almost went into genetics *sigh*...)

Corkey,

You misunderstand me if you think I'm attacking you (or anyone else for that matter) --as I stated above, it's my opinion regarding GMO in general. I offer the comment about scientific citation because that is the academic convention when discussing data and scientific studies. Since I am a trained scientist by profession, I can assure you I do not use words like "truth" to discuss science. Data is either accurate or precise, neither or both.

If you'd like to share your sources regarding the Monsanto GMO studies and bee colonies, I'd very much like to read them. Thank you.

http://www.naturalnews.com/035610_ho...orn_syrup.html

http://www.energygrid.com/ecology/20...ycollapse.html

http://solutionsforyourlife.ufl.edu/..._disorder.html

Part of the problem with talking about genetic engineering is that there's the science and then there's the business. I, and I think the other few voices here who are actually in favor of genetic engineering, are talking about the *science*. If Monsanto went out of business this very afternoon, it would not change one whit the promise of genetic engineering nor would it change the science behind it. I am not going to defend Monsanto. I am going to defend genetic engineering because the science behind it is extraordinarily sound.

As I said the other day, genetic engineering is the same thing we've been doing since we got the clever idea of trying to domesticate some plants and animals. The primary differences, the only real significant differences, are that we can do very targeted manipulations instead of, quite frankly, kind of stumbling about in the dark *and* we can cross the species barrier. That's it. Other than that, genetic engineering is the same process as breeders use except the traditional way is slow and only slightly better than random natural selection. For example, a while ago a Russian scientist did a truly elegant experiment to test the hypothesis that the domestic dog was closely related to the grey wolf and that humans selected for friendliness towards humans.

To test this, he took foxes (which are still canines) and only allowed those animals that were most friendly to humans to breed. Within startlingly few generations (less than 20) the foxes had floppy ears, more puppy-like behavior, and instead of the more uniform coats of the fox you got the more color-varied coat we see with domesticated dogs. All of these follow-on effects weren't being selected for, those genes just came along for the ride. So in the ways that selection has been done for the last 15000 years or so, lots of genes have come along for the ride.

People think that because one is 'natural' and the other is 'science' that one is better or different than the other but they are really not. Yes, we're taking genes from fish and putting them in strawberries or tomatoes but we're not taking the fish genome, we're taking a specific gene and moving it across the species barrier and that's all. The reason--the ONLY reason--that nature didn't hit upon the solution of anti-freeze for either strawberries or tomatoes is that both species (the wild variant obviously) came up with a solution for dealing with cold, namely seeds. They didn't *need* anti-freeze in the wild because they did not evolve in locations that were cold long enough for resistance to cold to be selected for and seeds did the job. Again, that's the ONLY reason why those species didn't hit on the trick the fish did--they never had the correct problem for which anti-freeze is the solution. Nature is not guided and it has no foresight. It can't see down the road and it can't back up and take a better path when some species hits upon something clever. At no time did nature think "anti-freeze in strawberries would be good, wait on second thought no". There's nothing to do that thinking. Also nature is not exactly concerned with maximizing species. It is simply concerned with genes being passed down generation to generation. Nature doesn't act for the good of the species, it doesn't even act for the good of the individual, nature acts for the good of the genes.

If we want to talk about Monsanto and its business practices that's one subject and I'll likely agree with a lot that is said. But we're talking about genetic engineering specifically, not what Monsanto is doing with it and the idea that there is good, solid, scientific support for an anti-GMO stance simply isn't true.

http://www.slate.com/articles/health...people_.2.html

Cheers
Aj

Thanks for those links Corkey, I look forward to reading them!

And thank you dreadgeek for your post too, it's important to always tease apart cause and effect, as well as in what context it exists too. I agree with your analogy, today's genetic engineering is merely a refinement of yesterday's advanced animal husbandry. (my apologies to you greadgeek, I'm quite oversimplifying your eloquence)

If anything, I think genetic engineering provides an avenue of precision as a technique unequaled previously in history--my hope is that it will unlock many of our most challenging problems in health / science and in the end, improve our quality of life in the most sacred and profound ways.

I was just reading a sample lesson plan in my science educator's magazine using a sandwich (or a picture of one!) to teach the principles of stratigraphy (determining the relative ages of rock layers, fossils and volcanic events using layering and superimposing). It included an opening activity, enquiry, practice, and closing. Figures, I would associate good teaching with food :).

This is last is why I try to explain the science. There's a lot at stake. I'm going to give just one example: Huntington's chorea. There is a gene on chromosome 4 that consists of a single 'word' CAG (you can, in some ways, think of a genome) that repeats over again. On average people have between 6 and 15 repeats. Any number of repeats up to 35 and you're fine. The trouble starts at 39 or higher. Here's Matt Ridley talking about how not only do we know what gene causes it we can predict, based upon the number of repeats at what age you can expect to start showing symptoms.

(Matt Ridley -- Genome: Autobiography of a Species in 23 Chapters)

Now, we don't know what the gene is actually there for but one day we will and when we do we will be able to manipulate the genome so that we can simply edit out all repeats above 35. We could test for it pretty much as soon as the woman realizes she is pregnant. When we can, we should.

That's the promise. It would be beyond sin if we turned our back on this technology.

Cheers
Aj

Literal Genesis Trial: Creationist Gimmicks Versus the Optimism of Education

The Guardian, for reasons I cannot begin to imagine, published an article summarizing the so-called Literal Genesis Trial being promoted by Joseph Mastropaolo. As reported, "A California creationist is offering a $10,000 challenge to anyone who can prove in front of a judge that science contradicts the literal interpretation of the book of Genesis."

http://www.huffingtonpost.com/michae...BNotifications

(this is just for Aj.....cuz it makes her as nuts as it makes me. My dad had a master's in natural sciences....he is probably rolling in his casket)

If I can ask you one other follow-up, does that same feeling (I don't know what to call it when you say your Native American side) apply to editing *out* genes? I ask that in the context of the Huntington's chorea example I gave a few days ago. Since we know that any number of repeats above 35 is where things start to go badly and there is *no* benefit to having 39+ repeats of the CAG motif on chromosome 4, editing out all repeats above 35 would prevent people from a rather horrible disease. Are you saying that just as you don't think we should be changing genes except in the long, blind process (which, in my mind, is pretty wasteful) of selection that we shouldn't edit out genes even if doing so would save lives? I'm trying to understand where the line would get drawn.

If inserting genes in is, for lack of any better term, against nature isn't editing genes out also against nature? If we apply the standard consistently (i.e. don't insert anything and don't remove anything) then aren't we condemning people who could otherwise be saved? Admittedly, it is perfectly natural to die of Huntington's. I will not argue that somehow it is unnatural. There are lots of fates that are perfectly natural but that I am glad we can overrule. I'm not ready to condemn people to a horrible disease starting at 27 just because they have 50 repeats of a gene on chromosome 4. There's no evolutionary benefit to Huntington's disease. It is simply one of those things where nothing nature says it *can't* happen so it *does* happen.

So why on Earth does the motif continue to show up in a small portion of the population? Why hasn't it been selected out? Because by the time you reach your late 20s, in the environments in which we evolved, you've already likely had children. Any gene for a disease that can, if you'll excuse the term, hold its horses until *after* you've had at least one child will tend to be able to ride along with the rest of your genome. After you've passed your genes on at least once, nature really doesn't have much use for you. Another way of putting it is that genes that cause diseases that kill you before you have a chance to reproduce are selected out. So all of the low-hanging fruit, from the gene's point of view, was selected out hundreds of thousands or millions of years ago. The genes for diseases that we see tend to strike after your early twenties which, in the EEA (Environment of Evolutionary Adaptation) was well into the average person's reproductive career. So diseases like Alzheimer's and Huntington's and heart disease and high blood pressure are all back-loaded toward the end of one's reproductive career. A bunch of fifteen year old people dying is a net-loss from the gene's point of view, particularly in the EEA. A bunch of 45 year old people dying is zero-sum from the gene's point of view. By 45 you've already reproduced a few times, your oldest surviving children are, at that point, adults. From the point of view of nature, you're now superfluous. Thanks for playing. Nice of you to leave some genes around. You're expendable, your genes are not. That's nature for you.

So unless we intervene using technology (selective breeding in humans, needless to say, is a road we should not even contemplate going down) then we're pretty much signing the death warrants of any person unlucky enough to have 39+ repeats of the CAG motif on C-4. That's the natural way. I think we should veto nature because I think it is wrong vis a vis Huntington's.

Cheers
Aj

I posted this in the Zombie thread....however it does belong here:

from HuffPo

Bats' Oral Sex Helps Prolong Copulation, Scientists Say (VIDEO)

http://www.huffingtonpost.com/2013/0...een&ref=topbar

http://news.yahoo.com/scientists-pos...205206362.html


Looking for dark matter.

You beat me to the punch on this the other day, Corkey. I started working on an explanation and it became a bit more complex. So, I wanted to ask would people find it helpful if I put together a short primer on dark matter, what it is and why it matters?

Cheers
Aj