Scientists create simple synthetic cell(nist.gov)
nist.gov
Scientists create simple synthetic cell
https://www.nist.gov/news-events/news/2021/03/scientists-create-simple-synthetic-cell-grows-and-divides-normally
143 comments
The approach of removing unnecessary parts from a genome to find the minimum brings to mind Muntzing. In the 1940s, Earl Muntz was a TV seller who reduced manufacturing costs by cutting out unnecessary components. He walked around the lab with diagonal cutters and snipped out components until the TV stopped working. He'd put the last component back and have a new lower-cost design. The TVs only worked in high-signal areas, but were much cheaper than the competition and sold a ton.
https://www.electronicdesign.com/technologies/boards/article...
https://www.electronicdesign.com/technologies/boards/article...
If you can create something living by a combination of non living parts, I think that would be an interesting first. All of the life we know of, presumably has living ancestors. Hence the notion of a "spark" of life that is passed on like the flame of a torch. If we can create life from raw parts and supply the spark ourselves, it increases the relevance of science. Suddenly the idea of sending seeds of ecosystems in the form of printers and data would become viable.
We didn't create life from nothing, but we can certainly get close. https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment
Close? Yeah no, I dont think so. The experiment was basically a complete failure. It just happens to be interesting to analyses what actually happened and why. Its also based on assumed condition on earth that are now consider extremely unlikely.
Once you have mastered the top-down ("is this really the minimum? Or is it a local minimum?") approach, then you could attempt to bottom-up with an end product very firmly in mind. This way, you could skip aiming for parts that you might have thought required which were in reality redundant, or secure the existence of a piece you had once thought superfluous.
After you had bottom-upped a few times, one might even try to figure out a necessary order for the steps and possibly gain some more insight into evolution that way.
After you had bottom-upped a few times, one might even try to figure out a necessary order for the steps and possibly gain some more insight into evolution that way.
As all engineering, it boils down to requirements. Mycoplasmata, from which JCVI-syn3A has been developed, is reported to "survive without oxygen", which means that it's not necessarily a "pure" anaerobic organism. We must assume that there has to be an existing mechanism that protects this bacteria from highly reactive oxygen. If the design requirements don't include surviving the natural environment, then that is one of probably many more areas to trim genetic "fat" from. However, I don't know much about their work on synthetic bacteria nor the environment used for it, so it's possible that the aforementioned mechanism to be already removed from its genes.
What do you mean? Like creating every protin without a ribosome? Why would you need to go to that lengths of artfical?
Seams to like you have to start from the top up in one way or another.
Starting from the complete bottom just seams over the top.
If you can figure out how to go bottom up, it will result in new innovations in microscopic manufacturing methods.
Or... you can just use the top up built cell to manufacture things. Why build your own nanorobots when there are pre made nanorobots that already works.
Because switching to a different chemical composition (not carbon based) is more likely that way.
I think it must be possible to create equvivalent functionality from more durable materials.
This certainly is scify, but imagine changing all your cells one by one to cells which can withstand wider temperature ranges, and corrode (rot?) half as easily.
I think it must be possible to create equvivalent functionality from more durable materials.
This certainly is scify, but imagine changing all your cells one by one to cells which can withstand wider temperature ranges, and corrode (rot?) half as easily.
[deleted]
Starting from the bottom means, you really did understand it all, once completed ..
> Starting from the complete bottom just seams over the top.
Is it really?
"What I cannot create, I do not understand." - Richard Feynman
And to clarify, currently the ribosomes are provided as part of the cell-free transcription/translation system. Additionally, amino acids, tRNA (plus tRNA synthetase), RNA polymerase, and a primitive energy source (ATP with some extra energy in creatine phosphate) are all provided.
Here are the components of the most common cell-free transcription/translation systems (PURE): https://www.nature.com/articles/nprot.2015.082/tables/1
"What I cannot create, I do not understand." - Richard Feynman
And to clarify, currently the ribosomes are provided as part of the cell-free transcription/translation system. Additionally, amino acids, tRNA (plus tRNA synthetase), RNA polymerase, and a primitive energy source (ATP with some extra energy in creatine phosphate) are all provided.
Here are the components of the most common cell-free transcription/translation systems (PURE): https://www.nature.com/articles/nprot.2015.082/tables/1
Yes. Starting from the bottom, we might in the process discover that 90%-99% of cell components are cruft/inefficient, and discover how to make cells 10 or 100 times smaller. Imagine being able to inject neurons in the brain that are 100 times smaller.
Couldn't messing around with these artificial cells expose us to the risk of creating some second order mutations in humans from accidentally introducing these cells to our microbiome from the lab akin to the COVID-19 escaping a 'gain of function' virus lab theory?
Maybe that's the beauty of it. Maybe now's exactly the propitious time to play fast and lose with these things. The world today is more prepared than it has ever been - the overall impact may not even register as an independent event and be taken only as another wrinkle to current pandemic.
...but for the record, the above is not an advice. Here's the mandatory and responsible advice: kids, have fun (with science), but wear the things to keep it safe!
...but for the record, the above is not an advice. Here's the mandatory and responsible advice: kids, have fun (with science), but wear the things to keep it safe!
It would be extremely unlikely that such an artificial cell could colonize humans in any way, and even more unlikely that such a cell would be pathogenic.
Source?
Look at the proportion of natural cells that can colonize humans versus those that can't. Similarly, look at the proportion of pathogenic organisms versus non-pathogenic organisms. Assuming the goal wasn't to produce a pathogen, I find it unlikely we'd produce one accidentally.
Here's hoping
Meh, if you are not doing the atoms yourself from leptons and quarks then I am not interested.
Man: “I shall create life from dirt, to show I am equal with you.”
God: “Get your own dirt.”
God: “Get your own dirt.”
Of course, there's a relevant xkcd: https://xkcd.com/378/
> Of the seven genes added to this organism for normal cell division, scientists know what only two of them do.
This gives you an appreciation of how little we know. I work in bioinformatics, and every one in the field will tell you that there's been an explosion in the number of datasets. However, try finding recent data on your condition of interest! The number of experiments grows incredibly fast, but we're not there yet to build a comprehensive model even of a simple organism.
This gives you an appreciation of how little we know. I work in bioinformatics, and every one in the field will tell you that there's been an explosion in the number of datasets. However, try finding recent data on your condition of interest! The number of experiments grows incredibly fast, but we're not there yet to build a comprehensive model even of a simple organism.
https://vizbi.org/Posters/Images/2021/vB26.png
They're working towards it :)
They're working towards it :)
I wonder if this is going to be incredibly useful or totally over the top for research. Imagine a development like the BioNTech vaccine. With an atomic-resolution cell simulator, you could verify your mRNA code, including the delivery into the cell itself and watch it perform.
But would that be like watching my CPU decode and fetch instructions, interesting but completely useless for most practical applications, or like a debugger introspecting a running process, an incredible useful tool?
But would that be like watching my CPU decode and fetch instructions, interesting but completely useless for most practical applications, or like a debugger introspecting a running process, an incredible useful tool?
IMO, an atomic-resolution cell simulator would be extremely useful.
If you have an atomic-resolution cell simulator, you can add lots of automatic interpretation to layer up the information. For example, you can use relatively basic inference software to get a list of metabolite interactions (and their rates and derivatives). An additional layer would contain inferences about the way those metabolites move inside the ER and so on.
Even with those layers, the amount of brain power needed to understand anything would be significant. We may not have enough experts or expert-years to accomplish much. Perhaps a further step would be to make the models more accessible to people with less specialization. Even find more playful names for cell metabolites, the ones we use right now are utterly unpronounceable.
If you have an atomic-resolution cell simulator, you can add lots of automatic interpretation to layer up the information. For example, you can use relatively basic inference software to get a list of metabolite interactions (and their rates and derivatives). An additional layer would contain inferences about the way those metabolites move inside the ER and so on.
Even with those layers, the amount of brain power needed to understand anything would be significant. We may not have enough experts or expert-years to accomplish much. Perhaps a further step would be to make the models more accessible to people with less specialization. Even find more playful names for cell metabolites, the ones we use right now are utterly unpronounceable.
> But would that be like watching my CPU decode and fetch instructions, interesting but completely useless for most practical applications, or like a debugger introspecting a running process, an incredible useful tool?
It would be like watching the cloud of electrons moving over transistors across an entire chip, without the benefit of knowing quantum mechanics. Except in this analogy, everyone is in the same boat and working on a single codebase that's the surviving vestige of billions of years of "just good enough" coders fighting it out, so every little bit helps.
It would be like watching the cloud of electrons moving over transistors across an entire chip, without the benefit of knowing quantum mechanics. Except in this analogy, everyone is in the same boat and working on a single codebase that's the surviving vestige of billions of years of "just good enough" coders fighting it out, so every little bit helps.
so fyi I worked in that lab, we called many of them MUFs ("membrane proteins of unknown functions")... We kind of suspect that all they do is maintain membrane integrity and isotonicity just by being present. One easy way for a cell to do to increase the yield of a stuff is to have literally more genes.
So there are a lot of interesting things to do (which I don't know if they did), like instead of having those last five genes in there, copying one of those five genes five times...
So there are a lot of interesting things to do (which I don't know if they did), like instead of having those last five genes in there, copying one of those five genes five times...
> One easy way for a cell to do to increase the yield of a stuff is to have literally more genes.
Wat
How does this work? Do they encourage expression of the genes that actually make stuff?
Wat
How does this work? Do they encourage expression of the genes that actually make stuff?
[deleted]
Maybe it's rather better to ruthlessly focus resources on a few things rather than know a little but not enough about everything.
This is an interesting result. Basically cellular biologists debugging cells the same way folks who don't understand how a program works debug it, by chopping parts off until it fails and then adding back bits one by one until it works again :-).
At some point, not today and perhaps not in the next 20 years, humans will understand exactly how cells and DNA "work" from first principles to final behavior. At that point, humans will either cease to age and never suffer from disease (Venter would have liked that), or humanity will be wiped out by a malicious organism that is designed by a deranged practitioner.
Yet another technology produced Lady or the Tiger challenge.
At some point, not today and perhaps not in the next 20 years, humans will understand exactly how cells and DNA "work" from first principles to final behavior. At that point, humans will either cease to age and never suffer from disease (Venter would have liked that), or humanity will be wiped out by a malicious organism that is designed by a deranged practitioner.
Yet another technology produced Lady or the Tiger challenge.
I had to look this up:
https://en.m.wikipedia.org/wiki/The_Lady,_or_the_Tiger%3F
https://en.m.wikipedia.org/wiki/The_Lady,_or_the_Tiger%3F
There's a fun Smullyan book with that title.
There's also epigenetics to consider, like methylation and acetylation, which adds a whole extra layer of complexity.
:/
I think it's really difficult not to underestimate the complexity, although software engineers have a unique perspective.
Have you ever maintained an application of vintage? You have some idea of how complex an application can get after a decade or two... Now, imagine an application which is X years old, where X is our age going back to the first ancestors...
Have you ever maintained an application of vintage? You have some idea of how complex an application can get after a decade or two... Now, imagine an application which is X years old, where X is our age going back to the first ancestors...
We already understand exactly how cells and DNA "work", the problem is methabolic networks are very large and hard to simulate with sufficient certainty.
That's rather the point. Those metabolic networks are not meaningfully separable from "how cells and DNA work".
> We already understand exactly how cells and DNA "work"
I must have read your comment differently than you intended, since understanding exactly how cells and DNA work implies that the first cell v1.0 would have divided as intended and that it would not have taken 5 years of painstaking research for v2.0.
From the article, "Of the seven genes added to this organism for normal cell division, scientists know what only two of them do."
I must have read your comment differently than you intended, since understanding exactly how cells and DNA work implies that the first cell v1.0 would have divided as intended and that it would not have taken 5 years of painstaking research for v2.0.
From the article, "Of the seven genes added to this organism for normal cell division, scientists know what only two of them do."
we understand the translation of DNA bases to amino acids, and we once though that was going to be enough to understand inheritance, but we're still unpicking additional mechanisms that regulate gene expression and post translation modification. There's heaps more turtles down there.
...and they also vary across groups of humans. We are not all the same.
Each of us is a n=1 genetic experiment.
Each of us is a n=1 genetic experiment.
Lol what are you talking about
Knowing how something works is not at all the same thing as knowing enough to make significant improvements. It's just a first step.
True, but knowing how something works enables you to walk the path to learn how to make improvements. It allows you to make reasoned changes vs random changes.
Maybe computer ‘will’, but not humans. We have had thousands of years to try to come up with a definition of life and free will, and we haven’t even managed that :)
https://www.quantamagazine.org/what-is-life-its-vast-diversi...
https://www.quantamagazine.org/what-is-life-its-vast-diversi...
It is important not to mix philosophical questions with pragmatic ones. We don't have a solid definition of what "life" is, but as this group demonstrated creating something that is unequivocally "alive" by our extant definitions.
Much like the COVID-19 vaccines are the first widely distributed "product" of our understanding of messenger RNA, I would expect the first widely available products that come from our understanding of building and operating single cell organisms to be things like water purification, drug production, Etc.
For example, an organism that secretes vanilla extract would be a multi-billion dollar product. And "all"[1] it would have to do is mimic what the vanilla Orchid does when growing seeds.
[1] This is a deep and wide void of knowledge about how it does what it does, not trying to gloss that over, just making the case for single cell organisms as useful products.
Much like the COVID-19 vaccines are the first widely distributed "product" of our understanding of messenger RNA, I would expect the first widely available products that come from our understanding of building and operating single cell organisms to be things like water purification, drug production, Etc.
For example, an organism that secretes vanilla extract would be a multi-billion dollar product. And "all"[1] it would have to do is mimic what the vanilla Orchid does when growing seeds.
[1] This is a deep and wide void of knowledge about how it does what it does, not trying to gloss that over, just making the case for single cell organisms as useful products.
Vanillin synthesis is mature technology.
E.g., France was said to export 12x as much "natural vanilla extract" as it imports, yet produce none at all.
Insulin production using microorganisms is likewise mature, although prices are kept artificially high.
Yeast produce rather a great deal of economically relevant ethanol.
E.g., France was said to export 12x as much "natural vanilla extract" as it imports, yet produce none at all.
Insulin production using microorganisms is likewise mature, although prices are kept artificially high.
Yeast produce rather a great deal of economically relevant ethanol.
JCVI-Syn3A has been around for a while. Here is the genome sequence from 2018 - https://www.ncbi.nlm.nih.gov/nuccore/1241355755
Back at FreeGenes we synthesized all of the genes from this organism with codon optimization for Escherichia coli (https://stanford.freegenes.org/collections/gene-sets/product...), the workhorse of synthetic biology. If you combine the right transcriptional and translational elements, you should be able to build a fully modular genome from this gene set! We also did a couple other organisms in pursuit of this modular genome. As a nice bonus, you can also easily do in-vitro cell-free experiments since the codon tables are nice (and I've heard from Kate Adamala's group that JCVI-Syn3 has pretty bad cell free, though that was a couple years ago)
It's important to note that JCVI-Syn3A has a LOT of problems when it comes to its practical use. There just isn't enough energy being put into making an understandable and practical modular/minimal genome.
Back at FreeGenes we synthesized all of the genes from this organism with codon optimization for Escherichia coli (https://stanford.freegenes.org/collections/gene-sets/product...), the workhorse of synthetic biology. If you combine the right transcriptional and translational elements, you should be able to build a fully modular genome from this gene set! We also did a couple other organisms in pursuit of this modular genome. As a nice bonus, you can also easily do in-vitro cell-free experiments since the codon tables are nice (and I've heard from Kate Adamala's group that JCVI-Syn3 has pretty bad cell free, though that was a couple years ago)
It's important to note that JCVI-Syn3A has a LOT of problems when it comes to its practical use. There just isn't enough energy being put into making an understandable and practical modular/minimal genome.
What is "pretty bad cell free"?
If you burst open the cells and extract all the goop inside, you can use that goop to express proteins. For certain organisms, like E.coli, this works quite well, and you can get a significant amount of protein. For others, like JCVI-Syn3, the goop sucks at expressing protein. So it’s a “pretty bad cell free” [expression platform]
So can we say science has finally achieved a biological “Hello World”?
Not exactly. These lines of cells weren't created from scratch. From the article:
> Scientists at JCVI constructed the first cell with a synthetic genome in 2010. They didn’t build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome. They called it JCVI-syn1.0.
> Scientists at JCVI constructed the first cell with a synthetic genome in 2010. They didn’t build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome. They called it JCVI-syn1.0.
"Hello World" isn't exactly created from scratch either. You're using libc in most cases.
Someone wrote it though. It’s not a blackbox that’s evolved independently for millions of years.
We as a species know how to build one, since we did.
I suppose this makes sense, but at a personal level, the two scenarios seem similar. Interpreters & compilers are blackbox to me, at least. I have no idea how they work, and I wouldn't be able to make one for myself. But sure, someone could teach me.
I'm curious if they are going to 'ship of Theseus' it. First replace the dna, done, then the lipid membrane, then feed it C13 labelled amino acids to prove that the entirety of the cell proteom is from their synthetic genes.
Not quite creating life but definitely hijacking it.
Not quite creating life but definitely hijacking it.
Not specifically with C13, but that is what is going on.
Exactly what i was writing!!! :)
Now, i guess that - like last time - we're going to have news everywhere claiming that scientists "created life" (again).
LOL
Now, i guess that - like last time - we're going to have news everywhere claiming that scientists "created life" (again).
LOL
Those gaps keep getting smaller and smaller though, don't they?
No, because like in JCVI-syn1.0
"They didn’t build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome."
In another words, like in the previous attempt (in which i was equally amazed - at first - only to then became disappointed latter) THEY DID NOT CREATE LIFE!!!
They picked up an already living organism and "reprogrammed it".
Its like having a computer. They are learning to program, and remove all the unnecessary parts but they still don't have a clue on to build the hardware.
The problem, it seems, is in transforming bare lifeless quimicals into something "alive".
Creating life, it seems, is still something reserved only to God Himself! (and i suspect it's going to be like that for a loooong time, if we ever manage to accomplish it anyway)
"They didn’t build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome."
In another words, like in the previous attempt (in which i was equally amazed - at first - only to then became disappointed latter) THEY DID NOT CREATE LIFE!!!
They picked up an already living organism and "reprogrammed it".
Its like having a computer. They are learning to program, and remove all the unnecessary parts but they still don't have a clue on to build the hardware.
The problem, it seems, is in transforming bare lifeless quimicals into something "alive".
Creating life, it seems, is still something reserved only to God Himself! (and i suspect it's going to be like that for a loooong time, if we ever manage to accomplish it anyway)
Intelligent Design as a theory for life’s origins has received a lot of unfair criticism because people think it’s code for “young earth creationism”. It’s not though, it’s an observation that random natural processes are too slow at generating information to be responsible for life on earth.
It’s the same deductive logic you would use if you found an artifact in the middle of the desert. Yes natural forces could have carved an image from the rock, but the more detailed the image the less likely it arose naturally.
The fact that even now, no one has any idea of how to create the basic forms of life shows the astonishing amount of information that exists in even a simple cell. It’s time to reconsider intelligent design, even if the designer is an alien species or a programmer of a simulation. There’s too much information to spontaneously generate, and we have never seen life come from non life.
The theory has been essentially banished from academia for political, not scientific, reasons, but Michael Behe and Stephen Meyer’s books, specifically Darwin’s Doubt and Signature of the Cell, lay out the case in detail.
It’s the same deductive logic you would use if you found an artifact in the middle of the desert. Yes natural forces could have carved an image from the rock, but the more detailed the image the less likely it arose naturally.
The fact that even now, no one has any idea of how to create the basic forms of life shows the astonishing amount of information that exists in even a simple cell. It’s time to reconsider intelligent design, even if the designer is an alien species or a programmer of a simulation. There’s too much information to spontaneously generate, and we have never seen life come from non life.
The theory has been essentially banished from academia for political, not scientific, reasons, but Michael Behe and Stephen Meyer’s books, specifically Darwin’s Doubt and Signature of the Cell, lay out the case in detail.
So if you say that alien scientists created life on Earth and is hence intelligent design, sure why not. Earth could be some alien civilization’s lab for all we know..
But then at some point those aliens, or the ones that created them, or the ones that ...... created them ..., must have been created spontaneously.
But then at some point those aliens, or the ones that created them, or the ones that ...... created them ..., must have been created spontaneously.
Totally, it just moves the problem but potentially moves it to a larger search space. If you find a piece of marble isolated on top of a cliff it’s not cheating to deduce that it came from a larger group of similar rocks. You would calculate the probability that it was formed there, vs the probability it was formed somewhere else and moved there.
I think there is a flaw in the logic.
Life forms spontaneously. Just because this life evolves into higher beings who can also create above life in lab, the fundamental fact that life formed spontaneously is not affected in any way.
Life forms spontaneously. Just because this life evolves into higher beings who can also create above life in lab, the fundamental fact that life formed spontaneously is not affected in any way.
It moves the question as to why is the fine constant exactly what it is to support life. If it was off by a billionth of a percent, hydrogen wouldn’t form, etc.
You are a cloud of atoms wondering about why the atoms exist.
You are a cloud of atoms wondering about why the atoms exist.
The fine-structure constant is only just known to that degree of precision. How far different it would have to be to interfere with known chemistry is much larger, maybe even a half-percent: that is, a half-billion times more than suggested.
We don't know what else could form, instead, with a different value; maybe even a better basis for life than what we got.
We don't know what else could form, instead, with a different value; maybe even a better basis for life than what we got.
> why is the fine constant exactly what it is to support life
Doesn't the constant depend on the type of life. I don't think we know enough to conclude that life everywhere in the Universe is similar, i.e. has a similar/same constant, as the life on Earth.
Doesn't the constant depend on the type of life. I don't think we know enough to conclude that life everywhere in the Universe is similar, i.e. has a similar/same constant, as the life on Earth.
Life forms spontaneously?
Where’s your evidence?
Is it not your position that all life on the planet has a common ancestor?
Or, do you believe there has been more than one ‘spontaneous’ emergence of life on earth?
Where’s your evidence?
Is it not your position that all life on the planet has a common ancestor?
Or, do you believe there has been more than one ‘spontaneous’ emergence of life on earth?
> Life forms spontaneously?
> Where’s your evidence?
It was a logical argument at a higher plane, at the scale of Universe. I do believe that all Life on Earth had a common/similar origin. Similar = there could have been multiple origins at different places on the planet Earth - I don't know if that has been proven wrong.
Perhaps I should have stated it as if life forms spontaneously....
The point is how far up do you want to go? Say for example:
Z was created by Y was created by X was created by W .... was created by A ... limit -> infinity
(where Z, Y, X ... are life on distinct planets)
At some point it will stop. So, how did the top most life form? It must have formed spontaneously.
If someone wants to call the topmost life God or Gods, who created them?
> Where’s your evidence?
It was a logical argument at a higher plane, at the scale of Universe. I do believe that all Life on Earth had a common/similar origin. Similar = there could have been multiple origins at different places on the planet Earth - I don't know if that has been proven wrong.
Perhaps I should have stated it as if life forms spontaneously....
The point is how far up do you want to go? Say for example:
Z was created by Y was created by X was created by W .... was created by A ... limit -> infinity
(where Z, Y, X ... are life on distinct planets)
At some point it will stop. So, how did the top most life form? It must have formed spontaneously.
If someone wants to call the topmost life God or Gods, who created them?
As articulated by most extant religions, that which is God is eternal.
Consequently, questions such as “oh yeah? Well then where did God come from?” are not persuasive. ‘God’ and ‘everything else’ are two entirely different categories.
Consequently, questions such as “oh yeah? Well then where did God come from?” are not persuasive. ‘God’ and ‘everything else’ are two entirely different categories.
It’s been banished from non religious parts of academia because it’s not falsifiable or testable, so it belongs in the theology department.
The ironic thing is that now many physicists are studying non-falsifiable theories like the multiverse.
I can’t find a complete version but the last minute of this clip from Silicon Valley nails that disconnect, the whole clip is spot on. (NSFW, language) https://youtu.be/TWoRVaGlFRc
My favorite test is to check whether life is anywhere else in the universe.
If we were to follow the science, then absolutely there is. But if you checked and there wasn’t?
Unfortunately it would take more energy than exists in the universe to travel and a check everywhere. :)
If we were to follow the science, then absolutely there is. But if you checked and there wasn’t?
Unfortunately it would take more energy than exists in the universe to travel and a check everywhere. :)
It is testable, if a scientist creates life in a laboratory then intelligent design exists. It is falsifiable, you can compute the amount of information contained in biological structures, and compute whether known natural processes can create that amount of information on the timescale of the universe. If they can, intelligent design is falsified.
Regardless, where the theory lives in the org chart is irrelevant to whether it is true or not, and it’s certainly no worse than all the other origin of life speculation.
Regardless, where the theory lives in the org chart is irrelevant to whether it is true or not, and it’s certainly no worse than all the other origin of life speculation.
>If they can, intelligent design is falsified.
That's not true, demonstrating that process A could have resulted in the observed effect does not show that process B did not cause it.
That's not true, demonstrating that process A could have resulted in the observed effect does not show that process B did not cause it.
If that’s true every paper that references life’s origins needs to be retracted. If natural processes can be responsible for abiogenesis then intelligent design becomes much less likely, which is as close to falsifiable as you can get for a statement of history.
The larger metaphysical claims are not testable. Some of the narrower claims are, such as that self-replicating evolvable structures cannot arise naturally.
This basically amounts to the claim that the complexity floor of life is too high for such a structure to arise naturally over terrestrial time spans.
Obviously a demonstration of abiogenesis would invalidate that claim. This could also be challenged by computational models that are sufficiently physically plausible, or the discovery or creation of even simpler lifeforms that extend the lower complexity bound of life down to regions that challenge the argument.
Of course another possibility is that this is our Fermi paradox answer: life is in fact so profoundly unlikely that its frequency of occurrence is e.g. less than once per billion years per galaxy!
This basically amounts to the claim that the complexity floor of life is too high for such a structure to arise naturally over terrestrial time spans.
Obviously a demonstration of abiogenesis would invalidate that claim. This could also be challenged by computational models that are sufficiently physically plausible, or the discovery or creation of even simpler lifeforms that extend the lower complexity bound of life down to regions that challenge the argument.
Of course another possibility is that this is our Fermi paradox answer: life is in fact so profoundly unlikely that its frequency of occurrence is e.g. less than once per billion years per galaxy!
Exactly, these are major themes in the books I posted. Darwin’s Doubt deals specifically with the Cambrian Explosion and the explosion of information over a short time span that it represented. It digs deep into the search space of protein folds and epigenetic information and whether known evolutionary processes can be responsible for the original emergence of the simplest forms of life, or if there are even simpler forms of life possible that lived before the Cambrian Explosion.
We don't know how much information was required for the Cambrian explosion because we don't have DNA sequence information from that era. We can only guess based on the DNA sequence information of today or from recent (in geological terms) fossils frozen in ice cores, etc. All the DNA sequence info we have is actually extremely recent.
It's possible that the very long "boring" period before the Cambrian explosion was in reality when a whole lot of stuff was being evolved that later all came together to allow large scale cellular cooperation.
An analogy I like is a barn raising. If you watched a barn raising from very far away it would appear that nothing is happening and then boom, you get a barn. In reality the structure is being assembled slowly on the ground for a long time before anything "macro" happens. This analogy also comes up in regard to macroevolution and perhaps even abiogenesis.
BTW it's important to remember that modern evolutionary theory does not include a theory of abiogenesis. Life is assumed to exist and evolutionary theory deals with how it changes over time. The origin of life is a separate (albeit related) scientific question and one for which we do not currently have an established answer. There are many credible hypotheses but so far no way to really test them.
It's possible that the very long "boring" period before the Cambrian explosion was in reality when a whole lot of stuff was being evolved that later all came together to allow large scale cellular cooperation.
An analogy I like is a barn raising. If you watched a barn raising from very far away it would appear that nothing is happening and then boom, you get a barn. In reality the structure is being assembled slowly on the ground for a long time before anything "macro" happens. This analogy also comes up in regard to macroevolution and perhaps even abiogenesis.
BTW it's important to remember that modern evolutionary theory does not include a theory of abiogenesis. Life is assumed to exist and evolutionary theory deals with how it changes over time. The origin of life is a separate (albeit related) scientific question and one for which we do not currently have an established answer. There are many credible hypotheses but so far no way to really test them.
I appreciate your posted alternative theory on this subject. It's refreshing.
Looks like you've been shadow banned? All of your comments are dead (check your post history in a private/non logged in window). I am not sure if you'll even get this reply!
I want to clarify the idea here.
1) We don't know how life originated on Earth.
2) We don't have a full idea of what happened during the Cambrian explosion.
3) We don't know how human consciousness manifests itself in the brain.
4) Evolution by random natural processes is not possible without deliberate nudges.
Is the claim here that 1-3 is simply not possible without an intelligent entity intervening in the natural laws? If so, I'm personally fine with it. God (who is the most popular potential Intelligent Designer) has always been a God of the Gaps. In the future, I am pretty confident we'll figure out the explanations using just the physical laws of the universe.
But if the claim also includes 4, then I think it can be discarded with a high confidence. We can already observe how evolution works at the virus and bacteria level. We have found the transitional fossils [0]. The science of evolutionary development biology [1] is already giving us great insights into how organisms translate the genetic code to build our complex bodies. It also shows how the same genes have been reused across species (e.g., the genes for eyes in the house fly and humans are the same). We don't need the Intelligent Design hypothesis to explain evolution.
(EDIT: I see from another comment that you already agree to the above point.)
The claim Intelligent Design supporters can make at best is that God created the first cells, perhaps nudged them a little during the Cambrian explosion, and perhaps again intervened before the evolution of Homo Sapiens. But all the rest happened the boring way, following the natural laws.
> we have never seen life come from non life.
Does not imply we never will. Given the countless other times this argument has been used to justify an Intelligent Creator when we didn't know something, I give very low credence to the idea that /this/ time is truly it. Unless someone can show mathematically why life cannot possibly emerge from the natural laws, naturalism remains the best hypothesis.
[0] https://en.wikipedia.org/wiki/Transitional_fossil [1] https://en.wikipedia.org/wiki/Evolutionary_developmental_bio...
1) We don't know how life originated on Earth.
2) We don't have a full idea of what happened during the Cambrian explosion.
3) We don't know how human consciousness manifests itself in the brain.
4) Evolution by random natural processes is not possible without deliberate nudges.
Is the claim here that 1-3 is simply not possible without an intelligent entity intervening in the natural laws? If so, I'm personally fine with it. God (who is the most popular potential Intelligent Designer) has always been a God of the Gaps. In the future, I am pretty confident we'll figure out the explanations using just the physical laws of the universe.
But if the claim also includes 4, then I think it can be discarded with a high confidence. We can already observe how evolution works at the virus and bacteria level. We have found the transitional fossils [0]. The science of evolutionary development biology [1] is already giving us great insights into how organisms translate the genetic code to build our complex bodies. It also shows how the same genes have been reused across species (e.g., the genes for eyes in the house fly and humans are the same). We don't need the Intelligent Design hypothesis to explain evolution.
(EDIT: I see from another comment that you already agree to the above point.)
The claim Intelligent Design supporters can make at best is that God created the first cells, perhaps nudged them a little during the Cambrian explosion, and perhaps again intervened before the evolution of Homo Sapiens. But all the rest happened the boring way, following the natural laws.
> we have never seen life come from non life.
Does not imply we never will. Given the countless other times this argument has been used to justify an Intelligent Creator when we didn't know something, I give very low credence to the idea that /this/ time is truly it. Unless someone can show mathematically why life cannot possibly emerge from the natural laws, naturalism remains the best hypothesis.
[0] https://en.wikipedia.org/wiki/Transitional_fossil [1] https://en.wikipedia.org/wiki/Evolutionary_developmental_bio...
Geology is killing evolutionary biology.
The time-frame established by Geology for the age of the earth is fairly firm.
Yet, our knowledge of the complexity of life keeps increasing.
While we keep uncovering additional scales of complexity in biology, the time in which it was supposed to have randomly occurred remains constant.
We ARE reaching the point (long past it, actually) where the mathematics demonstrate it is highly improbable that life as we know it today could have emerged from nothing in the limited timeframe imposed by the geologists.
To a skeptic, the evolutionist sounds like this: “It would take my program about 10 minutes to run through 2^N combinations.”
“How long if N was twice as large?”
“Ten minutes.”
“What if N is 100 times as large!”
“Still ten minutes! If you don’t believe me, you’re anti-science.”
“Maybe you’re anti-mathematics...”
“Lalalalla... I can’t hear you... here’s a link to a Dawkins video.”
“Yeah... whatever...”
The time-frame established by Geology for the age of the earth is fairly firm.
Yet, our knowledge of the complexity of life keeps increasing.
While we keep uncovering additional scales of complexity in biology, the time in which it was supposed to have randomly occurred remains constant.
We ARE reaching the point (long past it, actually) where the mathematics demonstrate it is highly improbable that life as we know it today could have emerged from nothing in the limited timeframe imposed by the geologists.
To a skeptic, the evolutionist sounds like this: “It would take my program about 10 minutes to run through 2^N combinations.”
“How long if N was twice as large?”
“Ten minutes.”
“What if N is 100 times as large!”
“Still ten minutes! If you don’t believe me, you’re anti-science.”
“Maybe you’re anti-mathematics...”
“Lalalalla... I can’t hear you... here’s a link to a Dawkins video.”
“Yeah... whatever...”
> We ARE reaching the point (long past it, actually) where the mathematics demonstrate it is highly improbable that life as we know it today could have emerged from nothing in the limited timeframe imposed by the geologists.
Well, do you have a source that does this mathematical calculation?
Well, do you have a source that does this mathematical calculation?
Sorry for your down votes. I'm grateful that you would share this perspective. As a Hindu, science and religion are not conflicting. I'm looking forward to reading those two books you cite - thank you for sharing!
The theory is banished because there is no supporting evidence for it - compared to evolution which has an enormous amount of supporting evidence. That's science working at its best, and nothing political.
I say this as someone who once believed as you do, that you've been fooled, perhaps like me, by not honestly examining the evidence for the other side with an open mind. May you also find enlightenment.
I say this as someone who once believed as you do, that you've been fooled, perhaps like me, by not honestly examining the evidence for the other side with an open mind. May you also find enlightenment.
Intelligent design is not incompatible with evolution, it deals with the origin of life not the process by which it adapts.
Ok... Let's put a end to this!
GOD CREATED LIFE!
There it is! I said it!
And I'm going to say even more: there is absolutely no scientific proof that shows otherwise.
In fact the complexity points keeps pointing this way. It's just a question of keeping the mind open. :)
Ok... You can now ban me for my comment!
GOD CREATED LIFE!
There it is! I said it!
And I'm going to say even more: there is absolutely no scientific proof that shows otherwise.
In fact the complexity points keeps pointing this way. It's just a question of keeping the mind open. :)
Ok... You can now ban me for my comment!
The complexity argument is tired. We can clearly attribute incredible complexity to the action of evolution.
Now it's true we don't have a good idea how abiogenesis happened, and it's possible it could have been a supernatural thing - although everytime we thought that so far we've been wrong.
As you point out we have no evidence to support that either, and assuming that ends further scientific inquiry. It's not a useful or helpful thing to believe even in the unlikely event it was actually true.
Now it's true we don't have a good idea how abiogenesis happened, and it's possible it could have been a supernatural thing - although everytime we thought that so far we've been wrong.
As you point out we have no evidence to support that either, and assuming that ends further scientific inquiry. It's not a useful or helpful thing to believe even in the unlikely event it was actually true.
Great! Now, how did your god evolve from non-divine material? Indeed, where can we find some divine material to experiment on?
Do I look like God?
Go ahead pray a bit and maybe He'll answer you those questions!!!
I surely don't know the answer, the same way scientists don't know how life was created in the first place. What everyone have is wild guesses and faith in those guesses. ;)
As to the material: First we should try to find out where to look for...
Go ahead pray a bit and maybe He'll answer you those questions!!!
I surely don't know the answer, the same way scientists don't know how life was created in the first place. What everyone have is wild guesses and faith in those guesses. ;)
As to the material: First we should try to find out where to look for...
Praying is about the most reliable way of not getting any answers.
But if you imagine it is simpler for condensed space dust to become divine than to become alive, then there is a certain bridge I am sure you will be eager to bid on.
But if you imagine it is simpler for condensed space dust to become divine than to become alive, then there is a certain bridge I am sure you will be eager to bid on.
That's a very different intelligent design to what I've come across. I guess people had to try to salvage it somehow.
You recommend Behe's book; I read his earlier book "Darwin's Black Box"a while back. I found it interesting, well-written, and superficially convincing but fundamentally flawed and ultimately a waste of time.
Thanks for actually engaging the arguments, do you remember what you found fundamentally flawed?
I read "Darwin's Black Box" over 20 years ago so I can't give a lot of details. His fundamental idea was "irreducible complexity", a system that won't work if you take away any piece, such as a mousetrap. He claimed that a lot of biological mechanisms were like this. The fundamental argument was that something irreducibly complex can't be formed by evolution because it won't work if is anything missing, so you can't evolve part way. E.g. a mousetrap that lacks the spring doesn't work at all. Therefore, evolution couldn't create the irreducibly complex mechanisms found in biology. QED.
The big flaw that I see is that he looks at the problem of creating irreducibly complex mechanisms by addition, but they can easily be produced by subtraction. As an analogy, an arch is irreducibly complex because if you take out any stone, it collapses, so you can't build it one stone at a time. But you don't build an arch this way. Instead, a support is built and the stones are put on top of the support, one at a time. When you take the support away, now you have an irreducibly complex structure. Similarly with biology, something can evolve step by step with redundancy, and then pieces are removed by evolution, ending up with an irreducibly complex mechanism that Behe views as impossible.
I should reiterate that I read the book decades ago so I'm probably wrong on the details of Behe's argument. I figured I should answer your question but I'm not particularly interested in having a debate on evolution.
The big flaw that I see is that he looks at the problem of creating irreducibly complex mechanisms by addition, but they can easily be produced by subtraction. As an analogy, an arch is irreducibly complex because if you take out any stone, it collapses, so you can't build it one stone at a time. But you don't build an arch this way. Instead, a support is built and the stones are put on top of the support, one at a time. When you take the support away, now you have an irreducibly complex structure. Similarly with biology, something can evolve step by step with redundancy, and then pieces are removed by evolution, ending up with an irreducibly complex mechanism that Behe views as impossible.
I should reiterate that I read the book decades ago so I'm probably wrong on the details of Behe's argument. I figured I should answer your question but I'm not particularly interested in having a debate on evolution.
The arch analogy is fantastic, thanks!
Me either just interested in other perspectives, thanks.
Yes ... using a copy and paste of seven existing functions, knowing what two of them do. Oh, and bootstrapped using a copy of an existing execution environment.
So basically the React tutorial app?
Only if we are shipping the cell with a 120MB node_modules directory.
Perhaps "Hello world copy and pasted from StackOverflow."
More like proof of concept of a buffer overflow vulnerability. It's smart but we have no idea what do all these transistors do
More like a quine, isn't it? Pretty impressive.
It's a 480 line (gene) Hello World. For this to be the minimum viable cell, when we don't even know what so many of the genes do, would be surprising to me. It would mean pre-cellular life somehow gathered these genes or equivalents without the benefits a cell provides. Not saying it's impossible, but it would be pretty interesting.
What would that mean?
I imagine that from engineering POV, having self-replicating cells that will also do the useful work won't be optimal. This self-contained single-cell system was the only one that could work in the wild initially, but after a while even in natural systems like our bodies we have cells (like those red ones from our blood) that are produced by specialized tissues (red bone marrow), are designed with a specific function and with a simplified structure (like to be small, without cell nucleus), and disposed by other specific tissues (in the liver). If I had to design a system (and a business) it would involve printing specialized (non-replicating) work cells and some control/disposal mechanisms. The research focus on simplest living and self-replicating cells looks interesting but not that much oriented on any practical purposes.
So grey goo version 0.01?
We are grey goo version 0.0.1!!! That is, life on Earth. Life has already become a solar powered self replicator that caused a global catastrophe, burying the whole Earth in a toxic gas.
I always get angry about the conservative idea that "It's hubris to think humanity is so powerful that we could possibly change the whole environment!" (occasionally sprinkled with "only god is that powerful")
Guess what? Such simple creatures as an early bacteria did it even harder over 2 billion years ago, making the earth nearly inhabitable by anything that came before it.
Guess what? Such simple creatures as an early bacteria did it even harder over 2 billion years ago, making the earth nearly inhabitable by anything that came before it.
Not all conservatives. There are some who actually advocate for a carbon tax.
Also, lots of religious people are socialist as all git-out, and some organizations advocate those political positions officially.
It's easy to hate on the stupid, uninformed conservatives. Just like it's easy to hate on the stupid, uninformed leftists.
Also, lots of religious people are socialist as all git-out, and some organizations advocate those political positions officially.
It's easy to hate on the stupid, uninformed conservatives. Just like it's easy to hate on the stupid, uninformed leftists.
Worth pointing out that the parent comment said conservative "idea", not conservative people.
Eh, this biological grey goo is likely so crappy at surviving that it would get snuffed out or out competed by any random culture from the bottom of your shoe.
I'd be more concerned about viral gain of function research and the weaponization of synthetic biology in general.
I'd be more concerned about viral gain of function research and the weaponization of synthetic biology in general.
Interesting development. We already use cellular machinery to make some drugs like human insulin made with genetically modified bacteria. I think an application for this type of development might be nano construction of advanced materials that are hard to manufacture in quantity, like an engineered bacteria to build sheets of the materials as long as it has a supply of graphite and minimal nutrition.
Stupid question from someone who has zero idea about this field :
What are the chances they unknowingly create a new virus/ bacteria for which no known defenses are present. How is this probability mitigated during design process and what protocols are followed for ensuring this doesn't happen. I did read about bio safety levels, but I feel they themselves could be bypassed.
What are the chances they unknowingly create a new virus/ bacteria for which no known defenses are present. How is this probability mitigated during design process and what protocols are followed for ensuring this doesn't happen. I did read about bio safety levels, but I feel they themselves could be bypassed.
Just think about the mass of all microscopic organisms outside the labs that suffer mutations all the time. Worrying about innocuous bacteria turning into something bad on accident within comparatively very limited environment of a laboratory doesn't make much sense. Think also of the many free floating bacteria cells in our environment that die due to various factors, whose bodies then have to break apart. Compared to what may happen in a lab, I imagine that those pieces of dead cells floating around freely may pose a greater risk of falling and fitting somehow within living host cells altering their function. (That's one of the mutation vectors, BTW, be it constructive or destructive.) The only scenario that makes sense to seriously worry about when a lab works with/on a virus or bacteria is if the material they started with carries inherently a high risk, or (worse) if they focus on weaponizing it (but that would not be "unknowingly" as you mention).
How much data is contained in the 500 genes of this cell?
I'm kinda curious the minimum number of bytes it takes to make a living cell.
I'm kinda curious the minimum number of bytes it takes to make a living cell.
543,379 base pairs = 1,086,758 bits = 135,845 bytes.
https://www.ncbi.nlm.nih.gov/assembly/GCA_001708325.2/
https://www.ncbi.nlm.nih.gov/assembly/GCA_001708325.2/
You don't need the other half of a base pair in your calculation
I believe that's two bits per base pair.
Thanks guys
Wow, so life even fits on the very first 8” floppy disk.
Wow, so life even fits on the very first 8” floppy disk.
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Ahh boy that title. Clicking on the link to probably realize that this is totally harmless and my initial reaction is due to how much I've been stuck inside for a year.
I've truncated the title to try to make it less baity. If anyone wants to suggest a better—i.e. more accurate and neutral—title, preferably using representative language from the article, we can change it again.
Could they make cells that can regulate, if there is abundance of X = do something? I mean that would end a lot of problems. Starting with diabetes.
For that to end diabetes, you'd need to keep the cells in the body... which has two difficulties: first, the cells need to be protected from the immune system destroying them and second, the cells need to find a place in the body to live... and then you have to find a way to keep their numbers regulated.
So at some point we can just print humans (or better organism) making organic life obsolete.
Stunning and beautiful: We are on our way to truly intelligently designed life.
"Truly intelligently designed life" would need to be designed by somebody truly intelligent. But all we got is us. So, that will always be beyond us.
Are we creating new organisms that can kill us?
We already do that ourselves naturally as an organism, as does the environment around us.
A simple synthetic cell is so far off from the myriad of potentially deadly cellular organisms(or even deadly malformed protein chains) that already exist and evolve right this instant that it's not worth a second thought in the context of "organisms that can kill us" for now.
A simple synthetic cell is so far off from the myriad of potentially deadly cellular organisms(or even deadly malformed protein chains) that already exist and evolve right this instant that it's not worth a second thought in the context of "organisms that can kill us" for now.
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[1]: https://www.nature.com/nchem/journal/v9/n5/abs/nchem.2644.ht...
[2]: https://pubs.acs.org/doi/abs/10.1021/acsami.8b10029
[3]: https://www.nature.com/articles/s41467-020-14696-0