The central dogma of biology

Introduction:These notes explain a process called the central dogma. Sometimes called gene expression. All life runs on some version of this process: General knowledge tells us all life runs on DNA, and we are made up of proteins. This demonstration shows how we go from the DNA to proteins.

For our new direction in science, we think a bit more detail is vital for the general public, and our policy makers. In the twenty-first century, when we are told that life runs on DNA, some of us are likely to yawn. Oh yes, heard that before, it's all okay, our scientists have that in hand. But we think it needs something extra.

DNA contains information in our genes, and, depending on the lifeform, what the lifeform is doing, in what environments, using what types of cells, that information is used to produce the required proteins needed at that particular time. Gene expression.

Reality: What's the current, major, view on the nature of reality. Tips: it's taught at Uni and schools. It's continuously on TV. And it exclusively dominates our major bookstores. Which view? ... "The whole Universe was in a hot dense state",,,,, and then ,,,, here we are to talk about it. It's Big Bang theory and evolution theory.

Evolution: When Darwin proposed his theory, it wasn't set in stone like it is today. There was a lot of discussion at the time, and, reading the origins literature, three prominent men were working on the same topics. Today, the evolutionists, obviously, have claimed Darwin, the creationists have claimed Edward Blyth, and the Intelligent Design people, it seems, have claimed Alfred Wallace.

Did you know that, when Darwin wrote his book, the word "Evolve" didn't mean, "transmutation of species". What did it mean? ,,,,,, The word was linked to the creationists ... It meant "to unveil", as in, unrolling of a scroll, gradually revealing information. The rumour is that Darwin didn't use the word in his first edition, because of that meaning and that connection, but he did eventually put the word in. For this reality check, we describe what the current paradigm says evolved from exploding gasses.

 

Definitions: For this presentation, we need those reading, and listening, to have a passing knowledge of the processes and concepts associated with, "Multiplexing", "Transducers", and "Turbines".

What's multiplexing? Zoom in to check out our visual aid on multiplexing, in the top, left of the above image. On our aid, visualise four phone lines coming into a microwave transmitter, being mixed (multiplexed), being sent as a single multiplexed signal, to the microwave receiver, where the signals are unmixed (de-multiplexed), from each other, and from any control signals.

This system is used in our tele-communications industries, and can also be used inside individual electronic systems. Multiplexing: A system where independent signals are mixed with a control signal, transmitted, and the information is recovered at the receiver end, and we receive our own phone call. It's called, "Mux" and "de-Mux", for short.

What's a transducer? For this presentation, we want you to be able to distinguish between detectors and transducers. Both are used in industry, and everyday devices, as input for automatic control. A detector is a device that detects a physical situation, and turns something on and off. Like an oven thermostat. But if we wanted a fancier oven, where we can have the temperature displayed, we need a transducer in the mix.

A transducer is a device that converts a continuously varying physical quantity, like pressure, flow, concentration, or density, into an electrical signal. These days, the large proportion of transducers have standard electrical outputs, to be readily suited for common, international, control systems. A very common transducer, that most people use, is the microphone, in our phone, to detect atmospheric vibrations as we speak.

We have made a lifeform for our training aid. Zoom in for a look (to the left of the multiplexing). How many inputs and outputs does this lifeform have? ,,,,,, Get the neurons firing ,,,,, There's two inputs and two outputs. Our bug is a smoke detector, so it will detect the presence of smoke, yes or no, and pressure on the test button, yes or no, and then two outputs, an audible and visual alarm. Internal power monitoring, and alarm. No transducers, but just chat on your phone and you'll be using one.

In our industrial systems, detectors and transducers are called digital and analog inputs. And with our modern computerized systems, the analog signal, from the transducer, goes through an analog to digital convertor, to interface with the other systems. Also, incorporated into transducers, generally, maybe there would be some sort of amplifier, and some sort of signal conditioning to produce a common interface.

For our industrial applications, besides the processing system, transducers enable our systems to be more specialized. The more transducers, the more complicated can be the process. For programming purposes, each input, whether detector or transducer, will be allocated a unique address, for the system to reliably access outside information, With that, the more inputs, the more processing power required.

Search on "prestin" for an example of a transducer in our body. It relies on a mechanical amplifier, a mechanical device to detect motion, and electrical processing to account for the logarithmic quantities involved. There are lots of transducers in our body, and millions of detectors. ???? ,,,,, Get the neurons firing.

 

What's a turbine? I'm hoping this is an easy one because turbines are used everywhere. Steam and water turbines in power stations, and wind turbines now coming on line, to produce renewable energy. Our training aid shows a turbine out of a truck turbo-charger. How is this turbine turned? ,,,,, Get the neurons firing ,,,,,,, it's exhaust gasses. ,,,,, What does it drive? Cue the thinking music ,,,,,,, a device to increase the density of the air going into the engine. From water wheels to turbochargers, turbines are a great invention.

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The Central Dogma (Gene expression): Okay, let's get into the central dogma. We need to mention that this process can get very complicated, directly after the opening statement. And we can also say, there are some very smart people out there, as in, how did they work that out. And then a minor complication: The person writing this is writing things outside his field of expertise. I'm hoping, in all of that, the reader will show me some mercy.

We have put some more bits out on our display. If we were talking this through, we would bring these out individually and talk about them as we placed them. But for this written version, we have put out the rope (white and brown), the four bits of timber, the coloured blocks, and the inside of my wife's old, worn out, sewing machine. Three blocks have one input, and one output, the ribosome has two inputs and one output.

The rope represents the software, DNA and RNA, the four blocks are the process, the coloured blocks are the hardware, amino-acids and proteins, and the sewing machine part is a reminder of all the inputs to the system. Remember, the type of lifeform, its cells, and its environment, etc, are all inputs to this process, and the inputs to the system, can instantaneously change what output is required. As in, what genes need to be expressed for a required protein.

Let's resurrect some knowledge of DNA: Besides maybe something else, it's the information to make proteins. The system is going to be prompted by internal and external signals, to go searching for the required information, genes, copy that information, use some form of that to make a string of amino-acids, and those are then transformed into the 3D protein shapes, shipped out to wherever they are needed.

Physically, DNA has the well-known twisted ladder format, with the information on the rungs of the ladder. The rails of the ladder are made up of ionic bonds, the strongest chemical bonds we know, and the rungs of the ladder use bonds similar to hydrogen bonds, one of the weakest chemical bonds we know. With this, you may have heard that DNA works like a zip when its information is being accessed. Built-in redundancy, with the double helix structure.

Those twists are twisted, and those twisted twists are twisted, on spools (histones), etc, to produce the 3D packing structure of DNA. The DNA and spools are called chromatin. Because it's a physical structure, with readers all over the place, sometimes DNA tears, or completely breaks. But there are gizmos that continually monitor the structure, and if any problems do occur, other devices do the fix-ups. The rumour is that a lot of DNA repair is done while we are sleeping.

The hierarchy of the information could be: Chromosomes, genes, words and letters. The chromosomes could be viewed as the larger, maybe visible under the microscope, structures. We're interested in the next layer down, the genes. Genes are divided up into exons and introns, (hit the search engines) represented by our brown and white rope, respectively. We are interested in the exons, because that's the data to make the protein.

We need another hiatus here because we're going to touch on something extremely complicated. As in, I will probably miss something, and, we could be here all year and still not have fleshed out all the nuances. So tick the positives, and after the content, and half an hour, you can web surf to your heart's content.

The exons (expressed regions) have words, called codons, and letters (bits) called nucleotides. With our computing, I don't know what word length we are up to, but for life, all words, codons, are three bits long, and there are four available bits. (A T C G for DNA, and A U C G for RNA). Our technology is based on two bits (ones and zeros).

Have you picked up on the structure of DNA? Exons, introns, exons, introns, etc. We say it's data and control, others may not. Where have we heard of that structure before? ,,,,,,, That's right, DNA is multiplexed information. And then the complications set in because it's not that simple. Exons can affect intron information, and vis-versa, as each is accessed and used.

Some other features: 1. For comparison of lengths, if exons were a finger long, introns might be our leg long, so most of the DNA is not data to make protein. All at nano-metres, I suppose. 2. Genes are not continuous stretches of DNA: It's something from here, and there, and there, etc, so genes, sort of, are set out like we use sub-routines in our programming. 3. The field of epigenetics tells us that lifeforms can adapt quickly by the DNA being bookmarked, and un-bookmarked, by the system, for different structures and processes, depending on the inputs, and these markers can be inherited by the offspring.

4. The bytes (The words) are three bits (The letters) long, and four available bits, letters, so do the maths. Those codes match up to the twenty amino-acids (or twenty-one, depending on who you are reading), stop/start codes, and some redundancy, to produce the thousands of proteins required for a lifeform. 5. Sometimes different gene regions overlap. We'll mention more complications as the information is processed. And then, 6. The massive storage capacity.

The information so far presented, and the emerging field of epigenetics, gives an insight in what's going on if someone says our DNA is 99 per cent the same as chimpanzees. We're both biological systems, similar proteins, DNA is the information for proteins, and epigenetics is telling us that there is more biological information in the lifeforms, somewhere, than in all of the lifeform's DNA.

 

Next step: We want some RNA: (Single stranded information) For this, there are thousands of reading heads running up and down the DNA ladder. We have named one as RNA polymerase, for short, but there are many types, and many names. As stated before, the system, prompted by inputs, starts searching for the required information, and when located, reads a start code, and starts coping the data from the double helix format into the single stranded transcripts of RNA. Stops when it hits a stop code.

There are many forms of RNA (The single stranded transcripts, copies, of DNA). We will only mention two. The one we show, going from RNA polymerase to the spliceosome, is the one mainly used in explaining the central dogma, and is called pre-messenger RNA. As seen on the training aid, it still contains exons and introns (intervening regions).

We give the reminder here that gene expression is continuous for the lifeform, and that's a wide range of conditions if we select a cell in a human, for instance. For us, some genes are only expressed for maybe a few hours, as we grow from a single fertilized cell, and some genes are expressed continuously, as we do all the things humans can do.

What's a spliceosome? As can be seen from our training aid, I hope, the multiplexed pre-mRNA goes into the spliceosome and the output is all brown. That is, the spliceosome cuts out the introns (the white parts) and joins all the exons (the brown parts) together (mRNA). Can you see why we had the multiplexing tutorial at the start? A spliceosome is a de-multiplexer, a receiver, exactly like with our technology.

One of the fun questions to ask at this point is, "Where is the multiplexer, the transmitter, if the DNA is a multiplexed signal, and the spliceosome is a receiver, a de-multiplexer, which prepares the data for input to our next stage, the ribosome?" ,,,,,,, Cue the thinking music ,,,,,, We're fairly sure it won't be found in this Universe.

Here are some more complications for this stage of the process. Exons can be skipped, introns can be left in, the same gene can produce different proteins, called isoforms, the same sub-sets of genes can be shuffled to produce different proteins, and the RNA can be altered, according to input signals, before it gets to the ribosome. Get the idea. What do we say? How do they know all that stuff? All we can just say is wow, and drop the jaw.

 

What's a Ribosome? Up to this point we have been looking at software, but this next stage starts looking at the hardware. Remember we are made of proteins and those proteins are made up of strings of amino-acids. The ribosome is a cell organelle that grabs a part, brought to it by tRNA, explained later, shown in above image, and attaches it to another part, according to a set of coded instructions fed into the organelle from the spliceosome.

So what is it? That's an easy question, in the twenty-first century. It operates like an automatic, industrial sewing machine, or an industrial robot. And the mRNA input is the machine code to programme the machinery, exactly like in industry now. The input process, with the two rope inputs shown, has something to do with comparing codon, with anti-codon codes where tRNA, another form of RNA, touched on later, prompted by the system, brings each amino-acid to the input of the ribosome.

So it can be seen that the ribosome is the very core of gene expression. The retrieved and processed gene information is fed into a nano-sized machine, and the raw parts are assembled, according to those instructions, to eventually be reorganized by the last process in the central dogma, the chaperones.

 

What's a Chaperone? We know what they are, but we don't know how they do what they do. Check out some images on the web and a chaperone is depicted as a container, with a lid on top. The string of amino-acids go in, the lid closes, and the correctly folded protein comes out. Magic stuff. Also, error detection takes place at this stage, as well as every other stage. The 3D structure is examined and if faulty, is unfolded and refolded into the correct shape.

Epigenetics is looking at this stage as well, because we could ask the question, "Where does the chaperone get its information to detect correct, or incorrect, shape, and to do the required fix-ups?" They don't think that information is to be found in the DNA. The terms primary, secondary, and tertiary structures are used in the context of chaperones, as the final assembly occurs, and all those steps require, possess, and apply information.

Folding is not completely understood, but when they do eventually understand the interdependent atomic forces involved, they will drop the jaw. What's that line of famous insight: In cells, "Everything, in everything, is controlling everything". Every part and process is linked to every other thing that is going on, as in, networking.

When chaperones are being described on the web, a lot of times the networking is mentioned, so we will mention it here as well. As can be appreciated, the proteins have to go somewhere, so some sort of addressing is probably involved. This is another source of information, and that's a bottomless pit. The information for all locations and processes used in, let's say a human body. Makes the head spin. In our systems, networks sit in the middle of our computing layers.

But yes, the body does it, via its cells, and systems, and does it all seamlessly in a healthy body. Input, from multiple types of detectors and transducers, prompt the use of multiplexed information (DNA), de-multiplexed (Spliceosome) and fed into automatic nano-robots (Ribosomes), where parts are assembled, and then passed on to be prepped (Chaperones) and shipped out to their required locations: The central dogma of biology. We will now put the rest of the gear on display, and put some finishing touches on our comments.

 

The Central Dogma of Biology: 1. Data storage and management. 2. Data retrieval and de-multiplexing. 3. Machine code entry and raw parts assembly. 4. Final assembly and distribution. That hot ball of gas did pretty well.

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Additional information: We have just finished the standard version of the central dogma, from an electrician's perspective: DNA, RNA, amino-acids, proteins: (DNA, transcription, translation, protein). And we've applied some modern, industrial terminology to those processes. But we would like to add an extra feature to the central process, and also add a power supply to the system. Shown in the picture above.

tRNA charging: To the central process, we can ask the question, "How does the tRNA pick up an amino-acid to take it to the ribosome?" We give this information because it wasn't easy to find, and when it was found it was extremely complicated. One of the toys to do this is called, "Aminoactyl tRNA polymerase III". Wow! the process is called aminoactylation, or tRNA charging. Please don't quote me.

They say it's the only place where the software meets the hardware. That's what the S / H means on that extra wood block. The tRNA goes, somewhere, I don't know where, directed in some way, I don't know how, picks up an amino-acid, I don't know how, and heads over to the ribosome, somehow. And remember, all twenty amino-acids, and their associated tRNAs, are doing this. All complicated, and all interlinked. That's our final bit of detail to the central process.

Software? Hardware? Inputs? Receivers? Data transfer? Data entry? Machines? For us today, in the twenty-first century, we know there will be an operating system, or systems, running somewhere. In our individual systems, the operating system is called the firmware, background programming, or "boot" system. Not like "Windows", operating at a higher level. "Windows", is called an operating system, but is still called software, and still needs firmware to run. I suppose, an operating system to run an operating system.

Networking: That block, which has networking written on it, five times, reminds us that each stage of the central process has its networking, and all of those are networked, and so forth. We also need to remember that all this is instigated by internal and external signals to the cell. Error detection and correction are also incorporated at every step of the process. All these processes make the operation of the cells, and body plans, a seamless whole. A fascinating and extremely thought-provoking process.

 

The power supply: We have the inputs, the process, and lastly, to complete a block diagram of some process control, we add a power supply. The power supply for all types of life, from bugs, plants to humans is called ATP Synthase. Again, what's the process we are driving? The production of amino-acid based lifeforms. Amino means using Nitrogen molecules. So, life: Nitrogen based lifeforms. Rewire the brain. Then check what's sticking out of our ATP Synthase on our training aid.

That's right, the power supplies for all life are run by turbines (proton turbines). Hit the search engines on, "rotational speed of ATP Synthase". You'll find it can run at a very high speed, maybe variable speed drive, maybe reversible. If you go hunting for how all of this is connected, the turbines are linked to the water, oxygen and carbon cycles on Earth. So the central dogma, is linked to ,,,,,,, the nitrogen cycle and could be viewed as the end result of digestion. The turbines, as the end result of respiration, but it's not that simple, because everything is interlinked.

I think the central dogma is called the anabolic processes, building up. Digestion, another incredibly complicated biological process, is called the catabolic processes, breaking down. After multiple processing steps, and where most of the amino-acids are processed, additionally, proton pumps strip the hydrogen atoms of an electron, and pump the protons across a barrier to produce the potential energy to run the proton turbines. Protons are used, exactly like water is used in our hydro-electric plants we use today.

The proton turbines connect, by a shaft, to a triple actuator which energises the spent ADP power pellets, into ATP, the energy currency of all life. The P stands for a Phosphorous molecule, and we are following the rumour that almost all of the Phosphorous in the Universe, is found on planet Earth.

Check out the composition of our atmosphere. About 80 percent Nitrogen (for the central dogma), about 20 percent Oxygen (for the turbines, as in, respiration), with a small percentage of trace gasses, carbon-dioxide being one of those. How do we get our intake of Nitrogen when it's such a non-reactive gas? The bugs put it into the soil, the plants take it out of the soil, and we eat the plants. The plants do that by using the photons from our Sun. All life is connected to the Universe.

 

Other items on display: Some of these are a reminder for me to talk about the wow factors in life and the Universe. 1. One of our wow factors not on display is the data density of DNA, which is way beyond our technology. 2. Just under our smoke detector bug, is a couple of proximity switches, to remind us of the speed of operation of the transducers and the control systems. Wow. 3. The bolts in that packet are made from titanium, to remind us of the depth of the Universe.

4. The packet to the left of the turbine is some leftovers from my wife's old sewing machine, to remind me to say, every part in the central dogma is precise, and has its part to play. 5. Those two discs, near the bolts, are out of a hot-water system. A reminder that physical objects contain information. One disc controls the hot-water temperature, at something degrees, and the other disc is for the high temperature cut-out. 6. The two gears? The central dogma is machinery. 7. Two dented chrome caps? Damaged goods, but still recognisable, and one's still useable.

8. Lastly, we picked a bug, e-coli, as an example of wow factors, and sampled some of the thousands of images on the web. E-coli run on some version of the central dogma, they have transducers, turbines, motors, solar panels, serial communications systems, and have some sort of symbiotic relationship with humans. That has to be a wow.

 

Relativity: There's a watch in the display as a reminder to say something about relativity. All amateurs, that's all of us, only need to know that time is linked to light and gravity. Eg, time on Earth runs different to our satellites because of Earth's gravity well. Relativity is a huge idea bomb for Big Bang theory. These days, time is seen as a fuzzy concept, and that relates to our concepts of reality, but that is never applied to Big Bang theory.

The watch is a broken watch so it only tells us the correct time twice a day. In our presentation, we will probably ask the question, "Using relativity, how do you make a working clock tick slower, and slower, and eventually stop, while other stuff keeps going, and then, starts ticking again, speeds up, and starts ticking normally, like everything else?" We leave that for you to think about. Seen in some movies today.

 

Looking at life and the Universe: We have two characters at the bottom left of our display. One could be a teacher, and one a student. They are looking at life and the Universe. They will be looking through the hi-tech transducers, through the central dogma, through the turbines, through the wow factors, and through relativity, at the depth to life, and at an awesome, and useful, Universe. Thank you for reading this.

 

New direction for education: From the above, we suggest that future biologists do some introductory modules in basic electrical theory, and industrial control systems. Industry giving insights to biology, and biology giving insights to industry. Maybe reassess the potential in that "hot, dense state".

Future: If you are in education, and you want to teach about life and the Universe, and the nature of reality, make sure to mention that life is based on advanced information technology and turbines, time is fuzzy, there is a fantastic, useful Universe out there, and the future is limitless. Get the neurons firing ,,,,, reassess evolution theory ,,,, reinstate that previous meaning of evolve and ,,,,, and let hope arise. Bert Poelstra. 26/5/2019.

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