Reflections: Curiosity driven.

This is our continuing project: The search for happiness, destiny and how to rescue souls. "CTU IV: Destiny calls". Enjoy.

Some of the following content will have a deeper context after reading Contemplate the Universe and Beyond the veil.

We are still collating the thoughts for "The Touch". The new topic is, "Destiny calls".

Henri

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I have spent some of the last few days on the web, researching how tRNA ends up carrying an amino-acid at one end, to be used by the ribosome during translation. A very frustrating job because everybody wants to either write about what tRNA is used for, or write about how mRNA is transcribed and used. Then, of course, if something is found, it's too technical for a website like this.

Remember the standard sequence of events is: DNA for some mRNA (Transcription by one of a number of polymerases), then amino-acids, then proteins (Translation by a ribosome). This process is called the Central Dogma. I have noticed that the overviews of how all this is coordinated are missing, or I can't find any.

Remember also, proteins are strings of amino-acids (polypeptide chains), folded in a particular way to do jobs in the cell. The different jobs available seem to be related to the various transcription factors used in the processes. The same gene can produce the variety of proteins, based on the feedback the cell receives from its environments. Don't quote me.

In that process, I was introduced to the fantastic typo, "amino-acid building blokes". Very funny, and is that good, it may have been done deliberately. Awesome anyway, and great for an Aussie. Not easy to write an error free document.

In the research, I had a partial win. The process is called tRNA charging (aminoacylation), and is performed by an enzyme called aminoacyl-tRNA synthetase III. Remember when we see the term enzyme we can translate that as "machine", and some writers do actually use that term. I assume this takes place in the body of the cell, not in the nucleus, but I haven't found out how the uncharged tRNA get out there. Some ATP energy is used to attach the amino-acid onto one end of the tRNA. So when writers describe tRNA as being used by the ribosome, they probably mean charged, aminoacyl-tRNA is used. Again, don't quote me.

I also found the gem where this process of charging, is the one and only place where the codes meet the protein sub-units, the amino-acids. Needless to say, that the term evolution is nowhere found with these articles. So a good place to start your own research on this, is to start with "tRNA synthetase", and go from there. Multiple holes to fill in that description, but it's a little more to add to the overview. We are starting to see how the table at the front of our book fits into the scheme of things.

Related to all of the above are the codons in mRNA and anticodons in tRNA, which have to match up during the translation process. We have written multiple thought bubbles on this but do not mention the term codon. But that matchup is the perfect example of a lock and key mechanism, and we've written heaps on that.

Henri.

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I decided to search on "protein folding" and, if you do the same, you will be introduced to "protein chaperones" and the term "proteostasis" (A composite word). A chaperone is a machine that folds the strings of amino-acids into their functional protein forms, and proteostasis is the name that has been given to the overall process to integrate all the chaperones. Their job it is to monitor all proteins (all proteins are called the proteome), looking at a protein's folded state, and if any problems are detected, do the fix-ups required.

And then, fantastic for us, start seeing statements like: "Integrated biological pathways", "Highly complex interconnection" and "A highly interconnected network that integrates the regulation of gene expression, signalling pathways, molecular chaperones and protein degradation systems". And yes, we've had a go at that topic a few times.

Where does networking sit in our IT hierarchy? Somewhere in the middle, so there's a world to uncover above and below the networking. Proteostasis relates to what networking happens at the cellular level. And then we are introduced to "Systemic stress signalling", which hints at the intercellular communications required from the higher functioning levels of the organism, to provide the information to be used at the individual cellular levels.

From a scientific standpoint, we can fairly confidently identify the physical layer in organisms: The atoms, subatomic properties, chemistry and physics. I'll have a guess at the application layer for us: It's the things we do: Work and play (not a rigorous guess). Yes, all the in-between to explore. What about "Contemplate the Universe"? We're fairly confident a scientific answer won't help with that question.

A lot of overviews can be gleaned from Cornelius Hunter's, "Darwin's God" blog site, I go there regularly and find the articles informative, and fortunately, they are from an evolution skeptic's point of view. I can only write the above because of that background.

Henri

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I've just searched on "RecA", prompted by a Cornelius post. If you do the same, you will be introduced to the world of "Homologous recombination" (HR) and "conformational proofreading (CPR)". You will find out that RecA is a large protein essential for the repair and maintenance of DNA, where, somehow, the system, maybe prompted through DNA polymerase, detects a broken strand of DNA, RecA grabs a broken end, and after some comparisons, maybe by CPR, with an intact strand, repairs are carried out. Don't quote me. The details become technical very quickly.

Some quotes on HR: 1/ "It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks (DSB)". 2/ "critical support for DNA replication". 3/ "indispensable for genome integrity". 4/ "three key steps: strand exchange, branch migration and resolution."

And then we read the lines, all this "... occurs naturally in eukaryotic organisms, bacteria, and certain viruses and is a powerful tool in genetic engineering", and, "enables populations to adapt during the course of evolution". They always stay on task: it's all natural, just vibrating atoms, and then they steal our engineer. And, of course, adapting is evolution. But, for us, adapting is the opposite of evolution.

Henri

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We are on our journey to find out a little bit more about body plans of organisms. On the weekend, I searched on "cellular differentiation", and was introduced to the term "growth factors", and, maybe, a specific one: "Ligand", and found the quote, "A ligand produced by one cell binds to a receptor in the extracellular region of another cell, inducing a conformational change in the other cell...". I interpreted that statement to mean: "Press the button or turn the key and the vehicle starts".

Other concepts covered are fertilization, ontogeny (The study of growth to maturity), the various stages: ectoderm, mesoderm and endoderm, for skin and nerves, bones and muscles, and other inside bits respectively. And then, of course, we find out that almost all cells, no matter what the type, have the same copy of the genetic code. It just depends on internal and external signals that are given for each cell to use in gene expression: How the data and control are managed for the final cell type and how it functions with all the others.

I had a good belly laugh because there was a diagram there, with the title "An overview of major signal transduction pathways." Absolutely no chance for an interested amateur to gain an insight on anything. Well, maybe one insight: No easy overview in sight. Lots to think about and yes, there are a lot of smart people out there. Ligands and receptors look interesting for some more research (Locks and keys, enablers and inhibitors).

It looks like ligands can work in three ways, that scientists know of. 1: Attach to a receptor in the cell wall. 2: Multiple bits are taken in through the cell wall by channels. And 3: Go straight through the cell wall.

And then the gem, for me. A ligand is, "an ion or molecule attached to a metal atom by coordinate bonding". Metals? Keys? Closely matched pairs? Yes, my spin on that is: Ligands are where utility meets complexity.

Henri

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Last night, on the ABC, I watched some of the show about how humans grow, from fertilization to old age. Not too many details, but they go through the gem that I have also read about in Cornelius Hunter's website. Somebody has found out (They have the rendered images) that, at the moment of fertilization, the potential embryo gives off flashes of light, I assume in the visible spectrum. Don't quote me.

I have a technical background, working with LEDs (light emitting diodes), optocouplers, and solar cells. So if we add the above information to the research that bacteria can communicate with each other via frequencies outside the visible spectrum, we can add optical communication to the metal keys, on how cells differentiate and communicate.

Henri

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Genesis 3:21. Immediately after the bad news, God supplied some clothes. Something had to die for God to provide the needed covering. The Hebrew word for "covering" is a rewarding research topic.

Isaiah 53:5-7. And by His stripes we are healed.

John 1:29. It was important to the Lord to identify with our humanity.

Revelation 5:5-7. It's one thing to plan something: Die for friends. But another thing entirely to carry it through. Even though a deity.

Henri

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Last night I searched on "glycans", prompted by another Cornelius post. My world exploded. We know that cells are surrounded by a hi-tech skin with channels and pumps embedded in it. But that is only part of the real picture.

Embedded in the outside skin (The plasma membrane) are millions of molecular strings called glycans. That word appears to be the fancy way to refer to sugar molecules. Other names are polysaccharides and carbohydrates. (Don't quote me)

These glycans are associated with signalling between cells and are involved in everything we could possibly imagine cells and lifeforms doing (Diseases, pregnancy, ontogeny, adapting to different ecologies, etc). So we can add those to ligands to help integrate the body plan. I think at this time, I could add the symbiotic bugs, like the TV programs love to always reminds us, to the growing list of integrated processes for a body plan.

I found out the glycans are a neglected research field because everybody wants to play with DNA and the associated processes. Glycans appear to be a bottomless pit, with endless variety, and no systems. And if there were patterns, they could be as diverse as fingerprints. I found the gem that the slime on fish is glycans. Amazing! Fish have armour, and then a high-tech sensor array all over their body.

Good hunting. Henri.

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For the last couple of weeks, I have been proofreading and tweaking "The Touch". It is now finished and on line.

Henri

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Oh pause,,, to meditate on good Friday.

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