The Incredible Process of Life (cd, videos, computer, component)

[NightBazaar]

Speaking for myself, when we think about who we are and what we are, how often do we think about the processes involved? Oh sure, we know we’re made up of cells, and it involves stuff called DNA, proteins, and so forth. But so what? What does all that stuff mean? What exactly is this stuff? What does it do?

The videos below give a brief glimpse of it in action. And the amazing thing is that these things have been continuously taking place as one long process for billions of years without stopping since the first beginning that led to the formation of life on Earth. Sure, there have been changes along the way, but you and I and everyone who comes after us are the result of this never ending process. This is the process that connects us with all other living things on the planet.

Admittedly, there’s a lot more to it than just that. But still, seeing it in this perspective, it’s like we’re all part of some kind of strange amazing factory that’s continuously been in the process of making this thing we call life. It makes us wonder how it goes from this to who we are. Not only are each one of us individuals with completely unique experiences, but we are also the end result of this constant process that began with your parents, their parents, and everything else that goes all the way back to the very beginning of when it all began.

Welcome to the strange and busy inner machine shop of your life. Please permit me to introduce you to yourself.




YouTube - How DNA Copies Itself




YouTube - From DNA to Protein




YouTube - BioVisions - The Inner Life of the Cell

[gy2020]

Those were amazing videos. It makes you ponder life.

[NightBazaar]

Yes, it really is a remarkable process. Seeing it in that way makes it look like something out of a surrealistic fantasy world that's completely alien to our ordinary, everyday views about life. Apart from all the necessary ingredients being present in the beginning, it makes me wonder why it all came together and do exactly as it did in the first place.

[bluepacific]

Originally Posted by NightBazaar

Yes, it really is a remarkable process. Seeing it in that way makes it look like something out of a surrealistic fantasy world that's completely alien to our ordinary, everyday views about life. Apart from all the necessary ingredients being present in the beginning, it makes me wonder why it all came together and do exactly as it did in the first place.

The animation helps to illustrate and make interesting the amazing process of things we do not see. It is amazing that they made reference to the term coined by Francis Crick with regard DNA . Specifically Crick's term is "The Central Dogma of Molecular Biology", they changed the wording in the video to "The Central Dogma of Modern Biology" and I understand why. There's been so much controversy and debates with regards the actual first origins of life, and a life that looks as simple as the components in the video, but are in actuality are far more complex than could have ever been imagined of understood by a Charles Darwin. That's why there is a desparate attempt to change what the wording of that doctrine states because it's an area that is usually avoided as far as any real viable discussion. Generally both sides of the issue can only come up with Fairytale versions, but I guess that's all either side of the issue can do since no eye witness was around to tell us the facts. Here's the traditional version of the central dogma.

Legend:
Transcription of DNA to RNA to protein: This dogma forms the backbone of molecular biology and is represented by four major stages.

1. The DNA replicates its information in a process that involves many enzymes: replication.

2. The DNA codes for the production of messenger RNA (mRNA) during transcription.

3. In eucaryotic cells, the mRNA is processed (essentially by splicing) and migrates from the nucleus to the cytoplasm.

4. Messenger RNA carries coded information to ribosomes. The ribosomes "read" this information and use it for protein synthesis. This process is called translation.

Proteins do not code for the production of protein, RNA or DNA.
They are involved in almost all biological activities, structural or enzymatic.

The Central Dogma of Molecular Biology

The story goes that on earth had a primitive environment and there was a prebiotic organic soup of protein molecules (I presume in the ocean) that first existed and began to do magical things in a bubbling mixture. Some protein molecules formed a membrane and other protein molecules trapped inside this membrane got bounced around and we have to assume several clung together and mysteriously became these primitive functioning cell components and at some mysterious point this first cell achieved some sort of self aware consciousness and became the first lifeform.

The problem is with all of the failed experiments thus far and even Crick's own Central Dogma shows us that it's impossible for proteins to be created without the information for doing so which is only encoded in the DNA . It's one of those chicken and egg controversies. Don't get me wrong, I'd love to see an experiment which could explain the actual mechanics of how it came about. Even Crick experimented with what he thought were the mechanisms for the 20 amino acids necesary for the formation of a protein molecule. He created a sterile environment with all the basic elements they guessed or imagined were there, and used an electrical spark to simulate the lightening, volcanos, etc that they thought could have been the driven energy force behind life formation. Interestingly he got four, but he had to rescue them from the experiment because continued electrical arching would have destroyed them. Still I find such an experiment interesting because I don't know the actual amazing processes any more than anyone else.

Then I wonder if it's actually possible to make an experiment without the intelligent fingerprints of a scientist and prove no manipulation by an intelligence. Even Crick later mentioned the impossibility of such and was resigned to an idea perhaps that life somehow originated from a panspermia type of explanation. I believe even Richard Dawkins said something similiar, but even he said that an extraterrestrial origin does'nt answer the question. This is almost related to the other thread of life on other planets.

Sad thing is that a man like Crick dies in 2004 in San Diego I believe and he takes with him all the ideas, research, speculations, dreams, imaginations, etc he never put down on paper for us to follow and we are held back until someone else comes along and makes new finds of something earlier speculated but never talked about.

Those animated videos are slowed way down for our benefit to grasp what exactly goes on inside a living cell. Someone might correct me here, but I think a good illustration of what was being done by those cells in the video was something similiar to the taking of a video CD and replicating it in a computer with CD burning software program and making more videos. What is even more amazing is that these cells, actually any cell does all of this at faster than supercomputer speed as compared to the slow motioned explanation we needed to grasp what we believe is going on. And it does it with accurate almost perfect precision. I believe that it was mentioned in one of the videos that it also has the ability to repair any mistakes which of course is true. And the cell also has available the 20 amino acid building blocks necessary for replicating more protein molecules, then directing how certain protein molecules will be specifically be used for a specific functioning purpose. Add to that our own human body and the control of our brain which controls by sending messages to the smaller DNA brain center which in turn controls the mRNA messengers which alert the ribosomes which translate and build. It's almost like a minature city or factory.

Understanding and observing what goes on is the easy part. It's the origin of the information encoded on the DNA that is the real puzzle. With CDs we know the origin of where they came from and replicating is not an issue, though most of us may not totally understand the actual process with what exactly goes on with CD burning software. We just see and observe the results of the newly created Cd and leave it at that. Still, it is interesting where such information, like the information inside the DNA of what Crick, Dawkins and others have said about the most primitive of known ameobas would fill over 1000 volumes of 600 page books of Encyclopaedia Britanicas. Again, where does it originate ???

[NightBazaar]

Originally Posted by bluepacific

Those animated videos are slowed way down for our benefit to grasp what exactly goes on inside a living cell. Someone might correct me here, but I think a good illustration of what was being done by those cells in the video was something similiar to the taking of a video CD and replicating it in a computer with CD burning software program and making more videos. What is even more amazing is that these cells, actually any cell does all of this at faster than supercomputer speed as compared to the slow motioned explanation we needed to grasp what we believe is going on. And it does it with accurate almost perfect precision. I believe that it was mentioned in one of the videos that it also has the ability to repair any mistakes which of course is true. And the cell also has available the 20 amino acid building blocks necessary for replicating more protein molecules, then directing how certain protein molecules will be specifically be used for a specific functioning purpose. Add to that our own human body and the control of our brain which controls by sending messages to the smaller DNA brain center which in turn controls the mRNA messengers which alert the ribosomes which translate and build. It's almost like a minature city or factory.

Understanding and observing what goes on is the easy part. It's the origin of the information encoded on the DNA that is the real puzzle. With CDs we know the origin of where they came from and replicating is not an issue, though most of us may not totally understand the actual process with what exactly goes on with CD burning software. We just see and observe the results of the newly created Cd and leave it at that. Still, it is interesting where such information, like the information inside the DNA of what Crick, Dawkins and others have said about the most primitive of known ameobas would fill over 1000 volumes of 600 page books of Encyclopaedia Britanicas. Again, where does it originate ???

I agree with many of your points. The purpose animation is to illustrate in order to better understand the process. I also agree that we're far from any complete understanding of the entire process. It's not just a single step, but rather a wide range of complex steps.

Although the first and last videos are slowed down for our understanding, the second video twice states what is shown (in that video) is in "real time". That's either wrong (twice?) or it is in real time. I'm not expert on the subject, so I have to say I have no idea if it's in real time or not.

And I'm with you: where indeed does it originate? How did all this come together in the way it did? We don't know. But it's fair to say that it goes a lot deeper than what is shown, because it also involves activity at the quantum scale.

Some speculations have suggested the idea of "panspermia", that is, this stuff may be out there in space. In a way, that's true, at least in that all the "stuff" is out there. I don't know if DNA necessarily exists in space or not, but certainly all the componants do. H2O, carbon, etc. Regardless, at the very least, the right ingredients and the right conditions enabled a beginning on Earth that has continued from the very beginning to the present time.

How and why it happened is indeed the Big Mystery. But I'm glad the end result has meant that I'm here, you're here, and everyone else is thriving on the planet. It's amazing that the process having developed over such an incredibly long period of time has led to the ability that we can think and wonder and ponder the meaning of our own existence.

[bluepacific]

Originally Posted by NightBazaar

And I'm with you: where indeed does it originate? How did all this come together in the way it did? We don't know. But it's fair to say that it goes a lot deeper than what is shown, because it also involves activity at the quantum scale.

I'm actually working with a group of researchers here in Sweden who are pushing for an alternative form of Physics (You know, one of those outside the box freakos with unconventional ideas) . In particular the molecular studies of water structure and it's various uses. The institute is headquartered in Malmö, Sweden just south of where I live in Göteborg and we'll be having a convention at the end of next month. This area of the country in particular has latched on to alot of this technology.

Originally Posted by NightBazaar

Some speculations have suggested the idea of "panspermia", that is, this stuff may be out there in space. In a way, that's true, at least in that all the "stuff" is out there. I don't know if DNA necessarily exists in space or not, but certainly all the componants do. H2O, carbon, etc. Regardless, at the very least, the right ingredients and the right conditions enabled a beginning on Earth that has continued from the very beginning to the present time.

Some have suggested Comets as a transportation system because of it's make up of water and perhaps microbes hopped on board for the ride. In the end it's all just good science fiction.

Water is a definite key to life. I'm just starting a thread on that very subject so I'll not corrupt this one here, but it's kool.

Originally Posted by NightBazaar

How and why it happened is indeed the Big Mystery. But I'm glad the end result has meant that I'm here, you're here, and everyone else is thriving on the planet. It's amazing that the process having developed over such an incredibly long period of time has led to the ability that we can think and wonder and ponder the meaning of our own existence.

My first interest and pursuit in life was Botany and despite what many may think a Botanist is, it's more than some guy who's a walking Sunset Western Gardening encyclopedia who's got a bunch of plants scientific names memorized. Although I have known quite a few who really are like that. I was speaking with an elderly Botanist here at the Göteborg Botanical Gardens about three months ago. We were discussing the very differences between an actual up to scratch avid gardener/nature enthusiast and and what a Botanist does and it really boils down to being trained to notice the most minute details of a plant. especially out in the field. There's always a feeling that you could discover something no one else has ever identified yet. It was this attention to detail that has led me to other areas of interest. I began to realize there are so many environmental variables and factors which influence life everywhere. Everything is connected. Suddenly I found myself interested in what is going on under the ground more than what was above. Hence mycorrhizae became my interest along with water. I had the land and room to experiment so I did just that.

BTW , here's an interesting puzzle which illustrates the impossiblility of any DNA being able to make any sort of improvement through (and here's another one of those oh so cherished words) Mutations. No matter what you believe one way or another, this game is kind of kool. It's brought to you by the The University of Utah's "Genetic Science Learning Center" and maybe you've seen this before, but for those who have not then here it is.

Let's just call it "Mutate a Sentence"

Originally Posted by University of Utah

A mutation is a permanent change in the DNA sequence of a gene. Mutations in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene.

How does this happen? Like words in a sentence, the DNA sequence of each gene determines the amino acid sequence for the protein it encodes. The DNA sequence is interpreted in groups of three nucleotide bases, called codons. Each codon specifies a single amino acid in a protein.
Mutate a sentence!

We can think about the DNA sequence of a gene as a sentence made up entirely of three-letter words. In the sequence, each three-letter word is a codon, specifying a single amino acid in a protein. Have a look at this sentence:
Thesunwashotbuttheoldmandidnotgethishat.

If you were to split this sentence into individual three-letter words, you would probably read it like this:
The sun was hot but the old man did not get his hat.

This sentence represents a gene. Each letter corresponds to a nucleotide base, and each word represents a codon. What if you shifted the three-letter "reading frame?" You would end up with
T hes unw ash otb utt heo ldm and idn otg eth ish at.

Or
Th esu nwa sho tbu tth eol dma ndi dno tge thi sha t.

As you can see, only one of these three "reading frames" translates into an understandable sentence. In the same way, only one three-letter reading frame within a gene codes for the correct protein.

Now, going back to the original sentence:
Thesunwashotbuttheoldmandidnotgethishat.

See how you can mutate the reading frame of this sentence by inserting or deleting letters within the sentence.

It's easy to make mutations that create "nonsense" sentences. Can you make mutations that maintain or change the meaning of the sentence without creating such nonsense?