I don't necessarily disagree with you completely. But I think your point is badly argued and perhaps unnecessarily harsh.
>As far as i know.
THAT is pretty much what it boils down to... WHAT do you know? HOW do you know it? Is it really fair of you to dismiss a position where one only seeks to know more than what you currently know?
>The very idea that some things outcompete others is one of our basic immunological defenses.
I don't know where you pulled this out of or where you're going with it. Perhaps a point can be made about host immunological tactics and responses to pathogens in the context of ecological adaptation and niches. But to draw some kind of connection via competition for resources is a pretty awkward and bizarre way of making that point. And what is purpose of bringing this up in the current context? Are you suggesting if our immune system doesn't need to handle something that can't compete in our ecological backyard, we shouldn't bother? I don't mean to put words in your mouth, but that is not a very scientific perspective.
>That we haven't seen something already.
>I doubt you'll find much outside of novel viruses because bacteria infest every corner of our world. around you, on you, inside you, above you and below you.
Are you sure you would know even if you were looking at it? Moreover, what are you looking with? If as it was postulated, a non-DNA based genetic code was used, our existing assays may not pick up anything at all. I'm not going to dive into a discussion about laboratory science just yet. But let's pull back for a minute and consider something even more conventional. There is a enigma in microbial ecology sometimes called "The Great Plate Count Anomaly" that simply stated is the fact many more microbial organisms exist than we can culture in the lab. Recent advances in metagenomic techniques has allowed us to sequence the DNA of these previously un-grow-able bugs and given microbiologists their first look at stuff they've never seen before. And this is only within the last couple of years.
New discoveries and advances are occurring much more recently than you believe. A few months ago, I came across a bit of relatively new research where modern techniques identified some symbiotic bacteria in the gut of an insect called the glassy winged sharpshooter which finally explained how it was able to feed on relatively un-nutritious xylem that lacked essential nutrients required for survival. It turned out there was a previously unknown microbial community in this hard to observe environment with different bacteria synthesizing different nutrients crucial for this insect's survival. Discoveries like this are possible because obstacles exist but researchers never stop asking how we can overcome the limits of existing methods and techniques. There are countless examples of such "things we haven't already seen" to paraphrase you. And I am confident that if we should dare to extend our search as was urged in the paper, we'll open up new door we can't even dream of at the moment.
I guess I can't really fault you for your perspective as it appears biology isn't your field of expertise. But for those of us bio-hackers here on slashdot, compelling questions of what we should be looking for and where/how to look for it, is most definitely "News for Nerds, Stuff that Matters". For the good of the community, I would ask that you and others not try to knock something simply because you don't understand it. Please try not to ask questions on the premise of unfounded assumptions.
That's a pretty narcissistic and arrogant world view which does little to advance the current state of knowledge. When we stop daring to think ambitiously and asking improbable questions about the world around us, we settle into a valley of complacency from which we loose the momentum of curiosity that has driven science and technological innovation. Imagine Einstein never bothered to write that letter which lead to the Manhattan project. Or if DARPA thought the packet switching ARPANET was a waste of time and money. Or if the DOE thought sequencing the human genome was someone elses responsibility.
Believe me, as a lab rat who's been doing bench work in molecular and cell biology for the last 3 years I am more qualified than anyone to sing the praises of our current power to probe the depth, diversity, and extent of life. It is easy for me to sympathize with those who are jaded by these routine "miracles" where we can send out a DNA sample and have it sequenced overnight. If we wanna know something, the answer is literally a bunch of mouse clicks and a few pipette pumps away. Not much to get excited about at all.
But any self respecting biologist who works with modern molecular tools and technique has seen the frightening pace of progress that has allowed us to do the previously unimaginable. For example, the 2007 Nobel prize was awarded for the development of the "knock-out" mouse. This has lead to all sorts of experiments that has elucidated protein (mal)functions that have lead to a revolutionary understanding of countless diseases and illnesses. In more recent years, we are poised for another such quantum leap with bacteria-derived "genomic editing" techniques such as TALEN and CRISPR that allows us to make precise changes in the DNA of model organisms.
If biologists have the mindset you espouse, that everything worth discovering has been found, none of these type of breakthroughs would be possible. I've talked to colleagues who often muse wishfully, "If only we can do ****** more easily, our experiment would be so much better." There isn't one among us who don't hope some newly discovered microbe from the deep ocean or where ever will lead to some new technique or method that will allow us to do different kinds of experiments to generate data we didn't think was possible to collect.
And that is not as far-fetched as it sounds. It has been pointed out before that more people have walked on the moon than been to the deepest part of Earth's oceans. Of the little bit we have seen down there, entire ecosystems run on biochemistry that might as well be from another planet. You think it is *easy* to go down there and do science on those critters? There is a reason why astronauts outnumber aquanauts and ease/simplicity isn't one of them. You can't just bring them to you either because, those organisms don't live in the kind of environment we operate most lab equipment.
And it isn't necessarily about who can out-compete who on this planet. Everyone gets to shine in the spot light because everyone potentially has a role to play on the stage of life. How unimpressed will you be if it is discovered that some newly identified ocean trench bottom dweller can help us clean up the "Deep Horizon" oil spill in the gulf of Mexico? Or what if some rare sparsely growing thing-in-a-rock synthesizes a potent life-saving anti-cancer compound? We are not out to make discoveries for something that can necessarily colonize and take over the planet. The motivation for such quests are as varied as life itself, but for me personally, it is about finding something that can be of use to humanity. New biology may mean our current tools/techniques don't work. But therein also lies opportunities for new technologies and new discoveries. And you can bet there will be spin-offs to spare!
Sure, it may be not much more than viruses we find out there. There may NOT be some exotic thing out there that confounds established biology of life. But who are YOU to say? Plenty of reputable scientists have expressed the sentiment, "That's impossible! Don't be so ridiculous!" only to eat crow as their more open minded colleagues scope them. All things being equal, I'd rather bet on the long shot with anticipation, open eyes, and an open mind.
At the moment, variations of the CRISPR-CAS system can only edit the genome of individual cells in vitro with varying efficiency. This is assuming you can culture the cells to begin with. For example, I work with human embryonic stem cells, which are particularly finicky. They won't tolerate much roughness and will even up and die on you if the growth conditions are just a bit off. This is very hard to achieve reliably as some culturing reagents (coating matrix, for example) are "undefined" products with variations in composition from batch to batch.
To go to a chop shop and treat your issue at the genetic level requires an in vivo way to introduce a CRISPR-enabled vector into your cells. This is not easy to do with today's technology, but it may not necessarily be a deal breaker. In the example you gave, a food allergy can probably be addressed by treating only the GI tract and the immune system that comes into contact with the offending allergen. As such, there is no need to target every living cell in your body in this case. However, if you are treating an illness involving a more fundamental life process, that is not the case. For example, a mitochondrial disease where basic cellular metabolism is defective would probably be best tackled when an individual is still a developing embryo or at least very, very young. Otherwise, tissues and organs that are not convenient to access will still retain the genetic defect and present problems for the host organism.
Another question is where in the genome you want to edit. So far, one of our experiments involving the targeted insertion (non-CRISPR method) of a construct into our hESCs have been a bust. Our best guess is that the intended site of transfection (sub-telemeric regions of chromosomes) is critical for cell survival and too much fiddling in the area is fatal. CRISPR-CAS was a compelling solution for us because of how ideally targeted it is supposed to be. We are not aware of anyone else who've used CRISPR with hESCs in the way that we are doing, but what has been reported so far with other experiments using notoriously difficult subjects has been encouraging. So far, the experiment shows clear evidence of true integration into the genome as opposed to a transient transfection. In about a week, a Southern blot verification will tell us if the integration was random or indeed targeted.
As rosy as I can paint a picture about what is possible, however, strong caution follows the introduction of any new technology. Anonymous Coward may be an asshole, but (s)he isn't wrong for being a cynic about the commercial deployment of this as a consumer product. Considering how complex human biology is, the chance of an unintended edit with unanticipated consequences is more than likely. Many genes are linked in very convoluted ways. Even with the human genome project having ostensibly mapped everything, we are still looking at just the tip of the iceberg. Having a complete manuscript, is very different from understanding all the nuances of the story. To get back to the spirit of your question, I would imagine that the scenario probably is more similar to dental service, where you go back periodically to check on the integrity of any major service, with tweaks along the way as necessary.
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Are there any useful avenues for tracking down forgotten developers? Should I go ahead if I can't find them? Have you ever had a situation where you needed something you knew was out there, but could no longer find?"
According to Falk, Shakespeare’s characters were connected to the cosmos in a way that seems quite foreign to the modern reader. Whether crying for joy or shedding tears of anguish, they look to the heavens for confirmation, calling out to “Jupiter” or “the gods” or “the heavens” as they struggle to make sense of their lives. "[Shakespeare] lived in an age of belief, yet a streak of skepticism runs through his work, especially toward the end of his career; in King Lear it reaches an almost euphoric nihilism. His characters often call upon the gods to help them, but their desperate pleas are rarely answered. Was Shakespeare a closet atheist, like his colleague Christopher Marlowe?"
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