NASA-Funded Research Creates DNA-like Molecule to Aid Search for Alien Life
In a research breakthrough funded by NASA, scientists have synthesized a molecular system that, like DNA, can store and transmit information. This unprecedented feat suggests there could be an alternative to DNA-based life, as we know it on Earth – a genetic system for life that may be possible on other worlds.
This new molecular system, which is not a new life form, suggests scientists looking for life beyond Earth may need to rethink what they are looking for. The research appears in Thursday's edition of Science Magazine.
[...] The synthetic DNA includes the four nucleotides present in Earth life – adenine, cytosine, guanine, and thymine – but also four others that mimic the structures of the informational ingredients in regular DNA. The result is a double-helix structure that can store and transfer information.
[Steven] Benner's team, which collaborated with laboratories at the University of Texas in Austin, Indiana University Medical School in Indianapolis, and DNA Software in Ann Arbor, Michigan, dubbed their creation "hachimoji" DNA (from the Japanese "hachi," meaning "eight," and "moji," meaning "letter"). Hachimoji DNA meets all the structural requirements that allow our DNA to store, transmit and evolve information in living systems.
Also at NYT, Discover Magazine, and ScienceAlert.
Hachimoji DNA and RNA: A genetic system with eight building blocks (DOI: 10.1126/science.aat0971) (DX)
Related: Scientists Add Letters X and Y to DNA Alphabet
Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
Synthetic X and Y Bases Direct the Production of a Protein With "Unnatural" Amino Acids
Related Stories
After a 15 year effort, scientists at the Scripps Research Institute in La Jolla, California have successfully added two letters to the usual DNA alphabet of adenine (A), thymine (T), cytosine (C) and guanine (G) common to all natural life on Earth. The new X-Y bases, d5SICS and dNaM, were inserted into an Escherichia coli bacterium where they replicated successfully for a week. When the supply of foreign nucleotides ran out, the engineered bases were replaced with natural ones.
From the article:
"What we have now is a living cell that literally stores increased genetic information," says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California, who led the 15-year effort.
Romesberg's group is working on getting foreign DNA to encode proteins that contain amino acids other than the 20 that together make up nearly all natural proteins. Amino acids are encoded by 'codons' of three DNA letters apiece, so the addition of just two foreign DNA 'letters' would vastly expand a cell's ability to encode new amino acids. "If you read a book that was written with four letters, you're not going to be able to tell many interesting stories," Romesberg says. "If you're given more letters, you can invent new words, you can find new ways to use those words and you can probably tell more interesting stories."
Potential uses of the technology include the incorporation of a toxic amino acid into a protein to ensure that it kills only cancer cells, and the development of glowing amino acids that could help scientists to track biological reactions under the microscope.
Researcher Steven Benner, at the Swiss Federal Institute of Technology in Zurich is attempting to engineer cells that can make the foreign bases from scratch, obviating the need for a feedstock.
The efforts of Benner bring to mind the immortal quote from Jurassic Park by Dr. Ian Malcolm:
"Oh, yeah. Oooh, ahhh, that's how it always starts. Then later there's running and screaming."
Researchers at The Scripps Research Institute (TSRI) claim to have created the first stable semisynthetic organism with extra bases added to its genetic code. The single-celled organism is also able to continually replicate the synthetic base pair as it divides, which could mean that future synthetic organisms may be able to carry extra genetic information in their DNA sequences indefinitely.
The cells of all organisms contain genetic information in their DNA as a two-base-pair sequence made up of four molecules – A, T, C, G (Adenine, Cytosine, Thymine, and Guanine). Each of these is known as a nucleotide (consisting of a a nitrogenous base, a phosphate molecule, and a sugar molecule) and are specifically and exclusively paired, so that only A is coupled to T and C is coupled with G. These nucleotides are connected in a chain by the covalent (electron-coupled) bonds between the sugar of one nucleotide and the phosphate of the next, which creates an alternating sugar-phosphate "backbone."
The team from TSRI have added two synthetic bases that they call "X" and "Y" into the genetic code of a E.coli carrier organism – a single-cell bacteria – and then chemically tweaked it to live, replicate, and survive with the extra DNA molecules intact.
The paper is available via PNAS:
Yorke Zhang, et al.,A semisynthetic organism engineered for the stable expansion of the genetic alphabet (DOI: 10.1073/pnas.1616443114)
New Natural Selection: How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
Before human beings wrote books or did math or composed music, we made leather. There is evidence hunter-gatherers were wearing clothes crafted from animal skins hundreds of thousands of years ago, while in 2010 archaeologists digging in Armenia found what they believed to be the world's oldest leather shoe, dating back to 3,500 B.C. (It was about a women's size 7.) For a species sadly bereft of protective fur, being able to turn the skin of cows or sheep or pigs into clothing with the help of curing and tanning would have been a lifesaving advance, just like other vital discoveries Homo sapiens made over the course of history: the development of grain crops like wheat, the domestication of food animals like chickens, even the all-important art of fermentation. In each case, human beings took something raw from the natural world—a plant, an animal, a microbe—and with the ingenuity that has enabled us to dominate this planet, turned it into a product.
[...] Modern Meadow's microbes can produce collagen much faster than it would take to raise a cow or sheep from birth, and the company can work with brands to design entirely new materials from the cell level up. "It's biology meets engineering," says Andras Forgacs, the co-founder and CEO of Modern Meadow. "We diverge from what nature does, and we can design it and engineer it to be anything we want."\
That is the promise of synthetic biology, a technology that is poised to change how we feed ourselves, clothe ourselves, fuel ourselves—and possibly even change our very selves. While scientists have for decades been able to practice basic genetic engineering—knocking out a gene or moving one between species—and more recently have learned to rapidly read and sequence genes, now researchers can edit genomes and even write entirely original DNA. That gives scientists incredible control over the fundamental code that drives all life on Earth, from the most basic bacterium to, well, us. "Genetic engineering was like replacing a red light bulb with a green light bulb," says James Collins, a biological engineer at the Massachusetts Institute of Technology and one of synthetic biology's early pioneers. "Synthetic biology is introducing novel circuitry that can control how the bulbs turn off and on."
The article discusses a number of topics, including microbe-grown collagen for leather, Genome Project-write, synthetic cells, a company using yeast to make perfumes and other products, and the falling (but still high) cost of DNA synthesis.
Related: Project to Synthesise Genes Mooted
Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
Scientists Create Independent Synthetic Cell With Smallest Known Genome
In 2014, scientists engineered Escherichia coli to incorporate new bases they called 'X' and 'Y' in addition to adenine-thymine (A-T) and guanine-cytosine (G-C). Now it has been demonstrated that these synthetic base pairs can be transcribed into RNA and used to produce a protein containing "unnatural" amino acids.
The addition of the new bases could increase the amount of amino acids from 20 to a possible total of 172.
A semi-synthetic organism that stores and retrieves increased genetic information (DOI: 10.1038/nature24659) (DX)
Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Previous efforts to generate such semi-synthetic organisms culminated in the creation of a strain of Escherichia coli that, by virtue of a nucleoside triphosphate transporter from Phaeodactylum tricornutum, imports the requisite unnatural triphosphates from its medium and then uses them to replicate a plasmid containing the unnatural base pair dNaM–dTPT3. Although the semi-synthetic organism stores increased information when compared to natural organisms, retrieval of the information requires in vivo transcription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA with a non-canonical amino acid, and efficient participation of the unnatural base pair in decoding at the ribosome. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions.
Previously: Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
Related: How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
(Score: 2) by MichaelDavidCrawford on Saturday February 23 2019, @02:24PM
Who's going to be the very first to inject this stuff into a _human_ stem cell?
To unleash a Hashimoji _virus_?
I advance the following hypothesis:
You read it here first, folks!
Yes I Have No Bananas. [gofundme.com]
(Score: 1, Funny) by Anonymous Coward on Saturday February 23 2019, @02:41PM
so when can i have my own personal "5th element" ^_^
(Score: 2) by Runaway1956 on Saturday February 23 2019, @02:58PM (18 children)
That's a problem with most Sci-fi. We can't imagine other life, so Sci-fi is rather lacking in alien life forms. But, ask yourself a serious question: Why would alien life be like our own? I'll grant that life in the neighborhood probably resembles our own life, but when you get out of the neighborhood? There are probably thousands of alternatives to our carbon-based DNA/RNA. And, there is no reason at all to believe that we would ever meet another mammalian species out there. Or, saurian, or reptilian, or even insectoid.
(Score: 4, Interesting) by Thexalon on Saturday February 23 2019, @03:55PM (8 children)
My understanding for why the eggheads expect other life to be carbon-based is because other atoms don't allow for the same degree of complexity as carbon does. It's not merely an assumption that nitrogen or silicon or something else kinda similar couldn't do the same thing, it's that they've tried chemistry tests and found that they don't work.
As for DNA, it's not like I'd expect DNA to be universal, but I would expect that ET life contains some means of transmitting data from one generation to the next.
There are some adaptations of earth-based life that have evolved multiple times and are thus likely extremely useful. Other than that, I don't expect any resemblance at all between ET life and T life. That said, life as we know it is in many species much weirder than anything imagined by sci-fi: I mean, octopi, jellyfish, coral, sponges, lichens, giant networks of underground fungus, I know they have some things in common but they're really a lot stranger to us than Klingons.
The only thing that stops a bad guy with a compiler is a good guy with a compiler.
(Score: 2) by EvilSS on Saturday February 23 2019, @05:01PM (3 children)
(Score: 3, Informative) by stormwyrm on Sunday February 24 2019, @02:44AM (2 children)
Boron is hardly what I'd call abundant in the cosmic scheme of things. It's actually a very rare element as it can't be made in bulk by any of the usual stellar and supernova processes, unlike carbon which is by contrast ridiculously common, since it is a direct product of stellar nuclear fusion. The universe started out with a lot of hydrogen and a little less helium, and very little of anything else. Given those two, stellar nuclear fusion can make hydrogen into helium, helium into carbon, carbon into nitrogen, etc. all the way up to iron, while stellar burning processes and supernovae can make even heavier elements. So just about every element in the periodic table can be made by those mechanisms, except for three: lithium, beryllium, and boron. The only known way these three elements can be made is from cosmic ray spallation [wikipedia.org] or possibly from the slightly less violent nuclear reactions in a stellar nova [soylentnews.org] (not a supernova, mind). I thus don't see it likely that boron plays much of a starring role in any form of alien life given its relative rarity. Though even so, remarkably, boron does seem to play a minor biological role [wikipedia.org] in normal earth life.
Numquam ponenda est pluralitas sine necessitate.
(Score: 2) by Pino P on Sunday February 24 2019, @03:58PM
Boron... rarity... Is that what made Milla Jovovich's character Leeloo from The Fifth Element so special?
(Score: 3, Interesting) by EvilSS on Sunday February 24 2019, @05:16PM
(Score: 3, Informative) by crafoo on Saturday February 23 2019, @06:57PM
Right. Also, some other compounds can form and be varied and complex, similar to carbon, but the energy required to form/break them up is higher. Or the reactions happen at much slower rates. Or they only form well in the presence of fairly rare solutions. Carbon-based life wasn't just a random roll of the dice. Or, well, it was of course, but as far as the chemistry goes it's the most likely given the most common conditions and relative abundance of the elements.
(Score: 2) by HiThere on Saturday February 23 2019, @07:59PM
It depends on the temperature range you're working on. At any particular range there aren't many good information storing linear molecules that are both stable enough, and unstable enough. And there are so many variables that it's hard to envision an alternative working system. You can bet, though, that if they find life in Titan, it won't be based on water and DNA. And DNA is quite unlikely...but that doesn't tell us what the reasonable alternative would be. We can guess that it will be only partially soluble in a non-polar solvent...but that doesn't narrow the field very much. We can guess that we're talking about some chain molecule, but THAT doesn't narrow the field much either.
So just saying it's different isn't very helpful.
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 2) by legont on Saturday February 23 2019, @09:01PM
I think it is more likely that there is only one kind of life around which migrated from one place to another. That's because the probability of self creating is just way too low for a single planet. Life migrates and does it often at different development levels.
Let's look at humans here. We have issues with joints and such and can't stand our sun without protection. Most likely we came from a smaller rock of a red star.
It's still possible that there are many variants. We may be a creation of some unethical hacker who shoot his half baked DNA design into space while escaping police.
"Wealth is the relentless enemy of understanding" - John Kenneth Galbraith.
(Score: 2) by edIII on Tuesday February 26 2019, @04:02AM
It's species of competing life adapting to their environments, which is why I don't suspect to see ET life resembling us much. It may resemble something on our planet, but not necessarily mammalian.
Life on our planet started in one environment, and then went though several stages. There's no guarantee that another world would've progressed the same way at all. We're changing the climate on the planet fantastically right now, which is only possible because trees evolved something nothing could eat at a time in our planet's history. IIRC, that's one of the reasons why we have these large reserves of oil, is because the planet kept accruing dead trees without the ability to convert them back into something useful for other life. Our exact progression depended on some variables that were provided by evolution itself, which is somewhat random. Like you said, some features have evolved multiple times within a species, and many times in several species or over long periods.
On top of that, you have the size of the planet, it's gravity, major minerals it's composed off, magnetic fields, tidal forces, etc. and you have even more variables that have to line up right.
I bet that if you reset Earth back to the beginning, it's not likely it would evolve the same way twice. I suspect that all of the randomness involved in our overall evolutionary process makes it unlikely for ET life to resemble us. It might be beating the odds to find something we can understand as other life, and certainly nearly impossible to be sexually compatible as popular sci-fi suggests.
Technically, lunchtime is at any moment. It's just a wave function.
(Score: 2) by takyon on Saturday February 23 2019, @04:26PM
Here's a reason: convergent evolution [wikipedia.org].
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 0) by Anonymous Coward on Saturday February 23 2019, @04:48PM
Clearly you have never met my in-laws. They are clearly some mutated alien/alternative life form. I assume the catalyst is my mother-in-law's meatloaf, though I am not brave enough to find out. :-/
(Score: 2) by EvilSS on Saturday February 23 2019, @05:05PM (6 children)
(Score: 0) by Anonymous Coward on Saturday February 23 2019, @05:25PM
no need to worry. thors sister took care of that.
(Score: 2) by takyon on Saturday February 23 2019, @06:04PM (4 children)
SG-1 had some pretty decent effects. Some of it looks goofy, other bits stand up well. Obviously they were cost-conscious. Many alien planets looked like the alien forests of Vancouver. Ship sequences were reused. Etc. And it still ended up being a pretty expensive show to make ($1-2 million per episode).
It's obviously much easier to have a full-scale humanoid alien since you can put a guy in a costume and makeup. The Asgard in SG-1 used a mix of puppets and CGI for some later sequences. But the trend of humanoid aliens in sci-fi goes back way earlier to 50s movies, Doctor Who, Star Trek, etc.
Now you have shows like Altered Carbon with absurd budgets and incredible looking special effects. Probably in the neighborhood of $5-7 million per episode [hollywoodreporter.com], reflecting heightened TV spending and an intense battle for eyeballs (if Netflix stops making original content, it gets steamrolled by established license holders like Disney). I would also point at shows like Sanctuary (starring Amanda Tapping) which mostly replaced IRL sets with CGI and green screens.
Going forward, we have stuff like real-time raytracing [soylentnews.org] that can be used to render a virtual environment around your green screen actors in real time. We also have technological paths [soylentnews.org] that could increase CPU and GPU performance by orders of magnitude. What costs Netflix $5 million per episode today could be done on a kid's computer in 20 years (machine learning and procedural generation can do the heavy lifting of creating a populated virtual world, you just adjust the parameters).
But there's one thing that won't change that much. The human imagination. It is easier for us to come up with humanoid alien designs, and it's easier for humans to relate to these designs. We like WALL-E because "he" is created in our image with human-like traits.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 1, Interesting) by Anonymous Coward on Saturday February 23 2019, @07:49PM (3 children)
actually "bad puppets" or mechatronics are in a way still more realistic then bad CGI.
the computer has to start from "nothing". so every cgi iteration needs to improve on itself to become more realistic.
with puppets, they come from reality and we can see it and we kindda know that because if that and our limited understanding of nature that somewhere in the universe the "puppets" might be real.
also making puppetts and mechanotronics teaches real life skills whilst a 20 year in the future computer program does not.
so hurry for puppets and robots!
p.s. any typos are due to this lenghty text eating into non growing input tezt bix (cannot see my typing) and the utterly shitty typing on android
(Score: 0) by Anonymous Coward on Saturday February 23 2019, @07:57PM (1 child)
ah, also young obi wan didnt like acting with imaginary co-actors that would only show up after he had done all his acting and maybe thats why some people didnt like the star wars origin episodes?
acting towards a puppet is\was easier for some actors -vs- thin air ... or maybe obi wan was still high from that previous movie that involved a imaginary train?
(Score: 2) by takyon on Saturday February 23 2019, @08:20PM
Some productions, including parts of the Star Wars prequel trilogy IIRC, use stand-in actors that are completely replaced by CGI later. Depending on how you do it, you can have your human Obi Wan reacting to a real guy in a body suit who is off camera, and then render a CGI model where necessary, or use the guy for motion capture purposes.
In the near future, we will see greater use of entirely virtual actors. This can lead to copyright/personality rights issues if you are trying to resurrect Marilyn Monroe or somebody, but you can always create a virtual actor from scratch or perhaps blend characteristics of multiple living or once-living people. Or you can simply ignore legal issues and bypass legally sanctioned distribution mechanisms. If you can animate and provide text-to-speech voice acting for completely virtual photorealistic actors, you can eventually provide lone wolves working on their 2035 desktop computers the ability to make a professional looking movie on a $0 to $10,000 budget (price of the computer and their free time essentially, maybe a little contract work to other people who are better at using the software, making music, etc).
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by takyon on Saturday February 23 2019, @08:09PM
Well we are now entering into the machine learning era where you can copy someone's movements (motion capture) without fancy suits, create photorealistic people that never existed, and other absurdities. Just the last 1-2 years has made a huge difference in the field.
This video came out 3 hours ago: AI-Based 3D Pose Estimation: Almost Real Time! [youtube.com]
This is the one I was looking for: This AI Learned How To Generate Human Appearance [youtube.com]
(you can see how the new one can complement the old one)
So yeah, animatronics/puppets/mo-cap definitely helped SG-1, Jurassic Park, Lord of the Rings (Gollum/Smeagol/Andy Serkis) and other productions. But CGI is continuing to forge ahead and will be combining with machine learning, ray-tracing, etc. For now I am predicting 1,000x and possibly 1,000,000x improvement in CPU/GPU/tensor computational power using new transistor designs and/or 3D architectures. We have not reached the end of the line yet.
There is still a demand for robotics-related skills. After all, where are the robots that will cook, clean, AND fuck? Or the robots that will replace factory and fast food workers using a common base model? Or the robotic boots on the ground for the police and military as well as wearable mecha suits? The answer is that all of what is commercially available is embarrassingly bad. There is still a long way to go. Sure, battery technology may be a limiting factor, but we should ultimately be able to make a robot that is indistinguishable in its appearance and movement capabilities from a human (not necessarily a design goal, but an aspirational one) even if it can only run for 5 minutes. Then work on improving battery energy density separately.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by crafoo on Saturday February 23 2019, @06:58PM (3 children)
Fascinating. Scary. Really kind of amazing to see this done. Also, this is how monsters are created!
(Score: 1, Interesting) by Anonymous Coward on Saturday February 23 2019, @08:04PM
theres a movie about that: misunderstood monsters. take your pick. some need a scream but laughter works too and theres another about a personified swiss mountain holiday retreat villain fighting against a zoo keeper with limited but transportable (and expandable) resources
(Score: 2) by HiThere on Saturday February 23 2019, @09:25PM (1 child)
Well, monsters that have a dependency on chemicals they can't get from a diet outside the lab.
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 3, Funny) by FatPhil on Sunday February 24 2019, @11:33AM
Great minds discuss ideas; average minds discuss events; small minds discuss people; the smallest discuss themselves