Scientists discover chemistry that may help explain the origins of cellular life • Hacker News Board

Re: Scientists discover chemistry that may help explain the origins of cellular life

#11

Post by tasty_freeze » Wed, Jul 24, 2019, 3:07 PM UTC

fergalish wrote: post #8

Since reading it somewhere in the distant past, I have become convinced that the moon played a vital part in the origin of life, by creating the tides. Picture a coastline in early Earth. Tide washes up a bunch of chemicals that get baked in a warm sun, while simultaneously getting exposed to a harsh atmosphere with plenty of energy surges (volcanic/atmospheric). Tide washes in a bunch of fresh chemicals to reiterate…

One thing arguing against this is that there was little free atmospheric oxygen, and thus little ozone. According to Nick Lane in his book, "Oxygen", UV light at the surface of the earth was 30 times greater then than now.

Life has had a lot of time to build up mechanisms to protect against UV light [1], including sophisticated dna repair mechanisms and creating sophisticated antioxidants and regulation mechanisms.

But at the dawn of life, whatever self-catalyzing reaction which constituted the first replicators would have been extremely fragile and unlikely to tolerate baking as you suggest.

[1] In David Goodsell's book "The Machinery of Life", p.112, he mentions that when you stand in the midday sun without sunblock, UV light can cause adjacent cytosine and thymine rungs on the dna to cross link to each other. A repair mechanism sweeps the dna looking for this exact bond to unlink it before it gums up normal dna transcription activity. How often does it happen? 50 to 100 times per second ... per exposed cell.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#12

Post by yehosef » Wed, Jul 24, 2019, 3:28 PM UTC

keithwhor wrote: post #7

yehosef wrote: post #5

The problem is that once you start to appreciate the immense complexity in a single, most basic cell, you realize how far away we are from understanding how life got started. This article would be comparable to some future generation trying to figure out how our computers were made and then stumbling upon factory that could make the cases. The case is important, but relatively trivial part of the machinery. Similarly…

Not really, no: semi-permeable membranes have the ability to spontaneously generate strong energy / concentration gradients and remove external interference from chemical signals. That's a necessity for life as we know it -- nearly all cellular chemical reactions are driven by concentration gradients across membranes. The "RNA World" hypothesis [0] and the flexibility of RNA as both a self-replicating and catalytic m…

> pretty convincing conceptual pathway

These phrases come up very often when discussing Origin of Life, but it's basically handwaving. It's like saying "we built a plane, which gives us a convincing conceptual pathway on how to get to the moon." The differences in complexities are sooo vast, there is really no comparison.

I can state it more clearly - We couldn't create a functioning cell from scratch (atoms) if we wanted to. I'm not talking about injecting/replacing DNA in an existing cell as Craig Venter et al do (which is impressive. You'll see many articles talk about "we built the first cell" or even add the words "from scratch" but this is what they did.)

I mean build all the functioning pieces - all the molecular machines (https://en.wikipedia.org/wiki/Molecular_machine) and other components. I don't even think we yet understand all the pieces.

You can read some of my questions about abiogenesis at https://biology.stackexchange.com/users/13238/yehosef - some of the questions and answers may highlight the complexity.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#13

Post by mensetmanusman » Wed, Jul 24, 2019, 3:37 PM UTC

fergalish wrote: post #8

Since reading it somewhere in the distant past, I have become convinced that the moon played a vital part in the origin of life, by creating the tides. Picture a coastline in early Earth. Tide washes up a bunch of chemicals that get baked in a warm sun, while simultaneously getting exposed to a harsh atmosphere with plenty of energy surges (volcanic/atmospheric). Tide washes in a bunch of fresh chemicals to reiterate…

The moon is the analogous cpu clock cycle for many biological processes.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#14

Post by ibraa » Wed, Jul 24, 2019, 3:37 PM UTC

yehosef wrote: post #5

The problem is that once you start to appreciate the immense complexity in a single, most basic cell, you realize how far away we are from understanding how life got started. This article would be comparable to some future generation trying to figure out how our computers were made and then stumbling upon factory that could make the cases. The case is important, but relatively trivial part of the machinery. Similarly…

I find it funny that people would rather believe in the matrix/simulation rather than God

Re: Scientists discover chemistry that may help explain the origins of cellular life

#15

Post by yters » Wed, Jul 24, 2019, 3:57 PM UTC

ibraa wrote: post #14

yehosef wrote: post #5

The problem is that once you start to appreciate the immense complexity in a single, most basic cell, you realize how far away we are from understanding how life got started. This article would be comparable to some future generation trying to figure out how our computers were made and then stumbling upon factory that could make the cases. The case is important, but relatively trivial part of the machinery. Similarly…

I find it funny that people would rather believe in the matrix/simulation rather than God

I'm not sure how the simulation theory even solves anything. It just pushes the problem to the simulator. I guess the assumption is maybe the simulator is much less complex, so makes the problem disappeared through our ignorance about the simulator, which is just the 'god of the gaps' fallacy in techno speak.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#16

Post by ggggtez » Wed, Jul 24, 2019, 4:22 PM UTC

apo wrote: post #3

A fascinating study that tries to solve the most difficult problem in the origin of life: bootstrapping. Nobody has been able to explain how the multitude of complex organic molecules needed to support life got there in the first place. It's a little like we're trying to reconstruct modern industrial civilization by assuming Dow Chemical exists whenever necessary. Dow and the entire chemical industry arose from a boo…

I really like the idea of this as a scaffold for collecting lipids for the first cell membranes. It seems likely to me that there would need to be some relatively simple compound responsible. The fact this is present in meteorites gives me some confidence that it must be a compound that forms fairly easily. Once again, the "improbability of life" just got a little more probable.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#17

Post by keithwhor » Wed, Jul 24, 2019, 4:30 PM UTC

yehosef wrote: post #12

keithwhor wrote: post #7

Earlier quoted context omitted.

Not really, no: semi-permeable membranes have the ability to spontaneously generate strong energy / concentration gradients and remove external interference from chemical signals. That's a necessity for life as we know it -- nearly all cellular chemical reactions are driven by concentration gradients across membranes. The "RNA World" hypothesis [0] and the flexibility of RNA as both a self-replicating and catalytic m…

> pretty convincing conceptual pathway These phrases come up very often when discussing Origin of Life, but it's basically handwaving. It's like saying "we built a plane, which gives us a convincing conceptual pathway on how to get to the moon." The differences in complexities are sooo vast, there is really no comparison. I can state it more clearly - We couldn't create a functioning cell from scratch (atoms) if we w…

We've never created a dinosaur in the lab like they did in Jurassic Park, does that mean no dinosaurs were ever spontaneously born?

You're right, biology is a complex field that, mechanistically, we don't understand all of the intricacies of from first (physical) principles. But invoking the simulation hypothesis as a reasonable substitute for what you, personally, believe is the unlikelihood of abiogenesis is functionally equivalent to suggesting Satan planted dinosaur bones underground to misguide our faith. I don't understand how you think, "could this be evidence of a simulation" is any less hand-wavy than, "RNA has catalytic properties that suggest lifeforms may have begun as RNA-based. In fact, there are viruses that self-replicate by hijacking cellular machinery that are entirely RNA. It's not unreasonable to believe that, given long enough timeframes, similar constructs may have spontaneously self-replicated, even if inefficiently."

The difference between biology and computation is that the mechanics of large-scale molecular systems are, in most cases, too chaotic with too large of a surface area of potential interactions to explain every step as a direct, in vitro replicable chemical reaction - we must approximate where possible. We have to rely on the properties of large stochastic systems, nearly unfathomable timeframes, and extremely rare events to explain most of the world we see around us today.

Yes, every element of the biological world is entirely unlikely. That's kind of the whole reason the field is so beautiful. It only works because there's just so dang much organic material, a constant and consistent heat lamp, and it's all been shaking around violently in a water bath for 3.8 billion years.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#18

Post by ibraa » Wed, Jul 24, 2019, 4:35 PM UTC

yters wrote: post #15

ibraa wrote: post #14

Earlier quoted context omitted.

I find it funny that people would rather believe in the matrix/simulation rather than God

I'm not sure how the simulation theory even solves anything. It just pushes the problem to the simulator. I guess the assumption is maybe the simulator is much less complex, so makes the problem disappeared through our ignorance about the simulator, which is just the 'god of the gaps' fallacy in techno speak.

The simulator is not less complex, the difference is that the simulator is not subjected to the same limitations/rules/laws of our universe.

You either choose the universe itself to be infinite (always have and always will exist) which contradicts all our observations about it, or you assume a higher entity (outside the universe) that is infinite (always have and always will exist).

The third option (nothing infinite) means we wouldn't exist at all, because if there's no "start" then you go into an infinite loop trying to find a start and nothing happens. But since we are actually here, then third option is out, and only the second option (higher entity) makes logical sense.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#19

Post by AtlasBarfed » Wed, Jul 24, 2019, 4:52 PM UTC

yehosef wrote: post #5

The problem is that once you start to appreciate the immense complexity in a single, most basic cell, you realize how far away we are from understanding how life got started. This article would be comparable to some future generation trying to figure out how our computers were made and then stumbling upon factory that could make the cases. The case is important, but relatively trivial part of the machinery. Similarly…

I think a fallacy, and this is not aimed at your comment, of intelligent design people is that because humans can't really comprehend the complexity of cells, biodiversity, and life chemistry, that it couldn't have arisen from somewhat basic preconditions and "bioalgorithms".

It's really a condescending bias in disguise. Because I, who consider myself awesome and smart, cannot decipher how this could have come into being, then it clearly must be the work of a deity.

To me, once you have mass scale evolution, such that you have ?quadrillions? of individual organisms doing their own survival calculations and experimentation over billions of years, then the amazing powers of the forms of life don't seem impossible.

It remains to be seen with all the habitable-zone worlds being discovered what is out there.

Re: Scientists discover chemistry that may help explain the origins of cellular life

#20

Post by ars » Wed, Jul 24, 2019, 4:57 PM UTC

ibraa wrote: post #14

yehosef wrote: post #5

The problem is that once you start to appreciate the immense complexity in a single, most basic cell, you realize how far away we are from understanding how life got started. This article would be comparable to some future generation trying to figure out how our computers were made and then stumbling upon factory that could make the cases. The case is important, but relatively trivial part of the machinery. Similarly…

I find it funny that people would rather believe in the matrix/simulation rather than God

The difference is that God wants you to behave a certain way, but a simulation doesn't.

People don't like to be told what to do, so they'd rather the simulation.

On a "what created the universe" level, they are both identical.