Origin of Life: Information within Life

In efforts done by origins of life studies, the simplest protocell that could be the source of living cells as we know it should contain DNA (or RNA), proteins & enzymes, all enclosed in a membrane. As simple as it may seem, this system, however, includes an advanced communication system. In the previous article, Origin of Life: Irreducible Complexity within the Cell we discussed the chicken-egg problem in that protocell. Now we will discuss the information evolution problem within this protocell, and generally in life as we know it. 

Information 

As per Webster’s dictionary: information is “the communication or reception of knowledge or intelligence.” 

In any communication system we find the core components: sender, receiver, communication medium, and the message or information to be communicated. Information is something imposed over the medium. It’s using the medium but it’s not the medium.  

Example: someone sent a message through morse code to another one, who broadcasted it over radio signals, which was heard by another one who transferred that message to an end user through mobile call, which was finally broadcasted through TV. The message or the information was sent multiple times using different materials. However, the information itself is non-materialistic. 

Similarly any software – which is an algorithm of saved instructions – is totally non-materialistic. Software is always running on top of hardware and relying totally on the hardware when communicating information or instructions between different nodes to perform certain functions. These nodes could be persons using the software or could be non-conscious machine parts that are programmed to send and receive information. The point about software is that: it’s designed and coded by human intelligence. 

Keeping these definitions in mind will help in the next part. 

Biological information 

DNA 

When looking at the DNA, most scientists like Richard Dawkins, Paul Davies, and John Lennox – regardless of their beliefs – admit that the DNA is a real code string. 

• Molecular sequence in DNA is not trivial or repetitive information (like ACACAC or GTGTGT, etc) 
• As DNA is a very long string of nucleotides, it could store an immense amount of information 
• The information within DNA is not merely Shannon information, but it’s meaningful and functional information 

• There’s great resemblance between the DNA codes, and computer software programs 
• There’s also great resemblance between the biological information flow and any modern IT communication system. 

DNA alone is not enough for life without being part of a context or a system that can read the embedded code and translate that into functional proteins in a process called translation. This exists in all life forms regardless their complexity: 

• each 3 DNA nucleotides or letters (called codons) translated through mRNA into 1 amino acid (out of 20 possible types) 
• a strain of a minimum of 50 amino acids are called Proteins 

Proteins 

All scientists today know that protein molecules perform most of the critical functions in the cell. Proteins build cellular machines and structures, they carry and deliver cellular materials, and they catalyze chemical reactions that the cell needs to stay alive. To accomplish this critical work, a typical cell uses thousands of different kinds of proteins. And each protein has a distinctive shape related to its function, just as the different tools in a carpenter’s toolbox have different shapes related to their functions. So Proteins look like the hardware used by the DNA software. The more complex the software is, the more complex is the hardware. 

• The average size of a protein increases from Archaea to Bacteria to Eukaryotic (283, 311, 438 respectively) 
• The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second 

• Viruses typically encode (from DNA) a few to a few hundred proteins, archaea and bacteria a few hundred to a few thousand, while eukaryotes typically encode a few thousand up to tens of thousands of proteins 
• It has been estimated that the average-sized bacteria contains about 2 million proteins per cell. Smaller bacteria contain fewer molecules, on the order of 50,000 to 1 million. Yeast cells have been estimated to contain about 50 million proteins and human cells in the order of 1 to 3 billion. 
• A short protein of 150 amino-acids can have 20¹⁵⁰ =  1.4 x 10¹⁹⁵ possible combinations. 

Design appearance 

Definition of design: The purposeful or inventive arrangement of parts or details. Or simply: the purposeful arrangement of parts.  

All scientists agree that life appears to be designed, even if some reject the design idea calling it an illusion, trying to find other alternatives. For example, Dawkins R. 1986. The Blind Watchmaker. New York: Norton.  

• P.1 “Biology is the study of complicated things that give the appearance of having been designed for a purpose” 
• p.21 “we may say that a living body or organ is well designed if it has attributes that an intelligent and knowledgeable engineer might have built into it in order to achieve some sensible purpose, such as flying, swimming, seeing … any engineer can recognize an object that has been designed, even poorly designed, for a purpose, and he can usually work out what that purpose is just by looking at the structure of the object.” 

In fact, the information system within life seems to be not just a product of engineering, but brilliant engineering. 

1. Communication within life appears to be designed like a fully integrated information system: 

• Within the cell itself, between different parts 
• Between organs 
• Information flow within living organisms is bottom-top and top- bottom as well 

2. Analogy between the information flow within the cell and any modern IT communication system: 

• DNA is Quadruple digital system (A, C, G, T), while in IT systems, it is mainly Binary (0, 1) 
• Codons (3 letters) , vs data bus in IT (8-bits, 16-bit, 32-bit, 64-bit, depending on the system) 
• start and stop codons, vs. header bits in IT standards to indicate the start and end of a message. 

3. The synchronization between senders and receivers within the cell implies a preexisting design, like: 

• codon length & DNA quadruple system to produce enough possibilities (64), versus the produced amino acids (20). If a smaller codon was used, we will have only 16 possibilities. That’s a mathematically pre-designed system. 

• The length of coded genes, mRNA and length of functional proteins, are all matching together. That’s an additional design aspect. 
• The “analog” 3D shape of protein which is critical to perform the required function depends on the amino acids formed by digital DNA codes. It is like any digital to analog converter. That requires a fully designed end-to-end system, correlating the desired function with the software codes in DNA. 
• Reversely, not every mutation in DNA or software random modification can lead to meaningful or successful protein, as functional protein formation is extremely rare (1 correct sequence for each 10⁷⁷ incorrect sequence – as mentioned by the molecular biologist Dr. Douglas Axe in his studies), thus the software code in DNA should be extremely precise to match the hardware (reference 7) 

Different opinions 

As evolution can’t explain how the first information system in life evolved (as mentioned in the previous article), Origin of life (or Abiogenesis) scientists made some trials to explain how information within cell might have evolved, however they are far away from reaching any possible explanation, and it all relies on imagination without observed experience supporting this imagination. Some of the hypotheses: 

• self-replication: that will lead to trivial information, while life is surely non-trivial, even in the simplest known or assumed form. 
• Pure chance: which is mathematically extremely improbable and was rejected later. 
• Necessity or Biochemical predestination, which was rejected as well as it leads to very simple information 
• Prebiotic natural selection, which is a self-contradicting hypothesis about the source of information, as it requires the existence of information in the first place so that natural selection can favor it 

• RNA world hypothesis, which still lacks the source of information – the source of the meaningful arrangement of nucleotides – within this primitive RNA, even if it is capable of partial self-replication. This will be discussed in the following articles in detail. 

The alternative idea is that information in life is really designed. 

• We never observed any communication system to evolve on its own. There’s always design and intelligence behind. 
• We infer design whenever parts appear arranged to accomplish a function or purpose, and we see definitive purposes and functionalities within cells and living organisms a lot. 

• Based on the analogy with computer codes and IT systems, it is more logical to think that this was intelligently designed, like what we do in computers and IT networks, than to just “imagine” a complete communication system – software & underlying hardware – emerging by itself out of nowhere. 

Conclusion 

Abiogenesis can’t explain till now how information evolved, nor how that advanced communication system within cells came into existence by natural processes. 

Based on observations, it’s more logical and scientific to conclude that information in life is the result of Intelligent Design. 

To read more about the “Origin of Life” series check: Darwin and the Origin of Life , Origin of Life: Irreducible Complexity within the Cell and What Is Life .

References: 

1. Richard Dawkins: Genes Are Digital Information – Evolution Podcast 01 – YouTube 

2. Paul Davies – “The Origin of Life” (C4 Public Lecture) – YouTube 

3. Origin of life and information – YouTube 

4. Stephen Meyer: DNA and Information – Science Uprising Expert Interview – YouTube 

5. Can Self-Organization Explain the Origin of Biological Information? – YouTube 

6. Can Pre-Biotic Natural Selection Explain the Origin of Life? – YouTube 

7. Information Enigma: Where does information come from? – YouTube 

Origin of Life: Irreducible Complexity within the Cell

Introduction 

According to Abiogenesis, it is assumed that the first life form was a simple cellular organism, which can evolve by itself during the prebiotic era, and then as time goes by, this simple cell starts to get more functions, being more complex, and forming more complex life forms.  

As we are discussing the origin of life, we should be more concerned about that assumed simple cell: how simple the cell could be? And what is the minimum abstraction that can be assumed for a cell to be alive? That is, what are the minimum required biological components to have a living organism? 

Basic components 

As described by Dr. Nita Sahai about The Origins of life (reference 1), the minimum basic components of Extant Life are: 

• Heritable, Mutable Genes (i.e. DNA) 
• Metabolic Cycles (i.e. Proteins and enzymes) 
• Boundary Membrane (i.e. lipids) 

However, the relationships between DNA, proteins, enzymes, and the cell’s membrane present a biological conundrum. 

Here we face multiple Chicken or Egg problems. 

• which came first: replication or metabolism? DNA or DNA polymerase Enzyme?  
• DNA/RNA coded information, or Cell Machinery that is capable of reading this information to perform all cell functions? 

• Enzymes are necessary for the timely formation of proteins, but these enzymes are built, in part, with proteins. 
• Proteins are required to create Ribosome Machines, but Ribosome Machines are required to create Proteins. 

The idea of having all of these components at once, at the same time, in the same place, joining together perfectly the first time, is extremely, EXTREMELY improbable. In addition to that, still multiple other issues are yet to be explained like: 

• The prebiotic chemical formation for the lipids, carbohydrates, proteins and Amino acids by natural processes (like chance, time and necessity) 

• The information, the instructions or the software encoding within DNA/RNA 

Irreducible complex system 

That leads us to a concept proposed by famous biochemist Dr. Michael Behe called “irreducible complexity”, which refers to a system that has a number of components, which interact with each other, to produce a function, that the components can’t do by themselves, and if you take one or more components away, the system doesn’t work, so it is irreducible. 

That concept can be applied to very simple cells, to larger Eukaryotes (organisms with cells with nucleus enclosed), organs, and entire organisms. This idea can be applied to machinery and equipment as well, as most devices are built from components, and there are core components that can’t be eliminated or otherwise the device will not function. Sometimes the overall idea is used to counter argue Darwinian evolution, but we are focusing here on the origin of life, showing how the biology of primitive cells exhibit irreducible complexity. 

The simplest forms of life are single-cell bacteria. Viruses are simpler than the simplest known cell and they lack the structures required to be alive as they reproduce only when their genes take over the host cell’s reproduction machinery. Nonetheless, even viruses require a minimum number of parts to function. 

It’s also getting clear that the living cell contains a lot of nano machinery, and using the term “machines” induces automatically: 

• The composition of parts (in which some are irreducibly complex) 
• Purposely functioning 
• Maintenance and correction and, accordingly, 
• Design 

Conclusion: 

Scientists have no proposal yet as to what the simplest cell should look like, or how the least required components come together to start that assumed cell. 

The living cell looks like it was designed, functions to achieve a certain purpose as if designed, and contains parts working together in harmony as if designed. That’s because it really is designed. 

Some further examples: 

• Bacteria Flagellum (reference 3) 
• Microtubules (reference 4) 
• DNA copying machines (reference 5) 

That term “machines” has been widely used in a lot of articles with titles like: 

• The cell as a collection of protein Machines: preparing the Next Generation of Molecular Biologists, Bruce Alberts 
• Polymerases and the Replisome: Machines within Machines, Tania A Baker and Stephen P Bell 

• Eukaryotic Transcription: An Interlaces Network of Transcription Factors and Chromatin-Modifying Machines, James T Kagonaga 
• Mechanical Devices of Spliceosome: Motors, Clocks, Springs, and Things, Jonathan P Staley and Christine Guthrie 
• Molecular Movement inside the Translational Engine, Kevin S Wilson and Harry F Noller 
• The Hsp70 and Hsp60 Chaperone Machines, Bernd Bukau and Arthur L Horwitch 

References 

1. “The Origins of Life: From Geochemistry to Biochemistry” – YouTube 

2. Irreducible Complexity – YouTube 

3. Amazing Flagellum : Michael Behe and the Revolution of Intelligent Design – YouTube 

4. Ron Vale (UCSF, HHMI) 1: Molecular Motor Proteins – YouTube 

5. Drew Berry: Animations of unseeable biology – YouTube 

For more articles about faith and science check: Origin of Life: Synthetic Life and Darwin and the Origin of Life

Origin of Life: Synthetic Life

Were scientists able to “create” life?  

In May 2010, a team of scientists led by Dr J. Craig Venter became the first to successfully create what was described as “synthetic life”.  

Dr. Venter is an American biotechnologist and businessman, known for many remarkable contributions in the field of genetics. 

The experiment to create life was done by synthesizing a very long DNA molecule containing an entire bacterium genome, and introducing this into another cell. The single-celled organism contains four “watermarks” written into its DNA to identify it as synthetic and to help trace its descendants. The watermarks include 

• Code table for the entire alphabet with punctuations 
• Names of 46 contributing scientists 
• Three quotations 

• The secret email address for the cell 

The synthetic life project went through multiple phases 

• First, the team edited an existing DNA and inserted it into another living bacterial cell 
• In 2010, they created & designed the complete DNA and introduced it to genomically emptied bacterial host cells. The host cells were able to grow and replicate. The resulting new organism was called: The Mycoplasma laboratorium 

• In 2014, they extracted the E-coli genome, and replaced it with a chromosome that has an artificial expanded genetic code 
• The team is still continuing the efforts to create new synthetic forms of life, as variants of the bacteria E-coli. 

These efforts provide massive applications like manufacturing pharmaceuticals and detoxifying polluted land and water. 

However, that new “synthetic life” was not made by humans out of non-living components, because: 

• In the process of assembling the DNA molecule, a lot of enzymes and components were taken from other living cells 

• The information within the DNA itself, a lot of it was learned, copied or replicated from existing DNA codes 
• The host cell is still a living cell with pre-existing capabilities of reading the codes in the DNA and producing protein accordingly, so it’s more like replacing its original software by another customized one 
• All these efforts are still focusing on simple single cellular organisms, as other forms of life are extremely complex 

In other words, a living “artificial cell” has been defined as a completely synthetic cell that can capture energy, maintain ion gradients, contain macromolecules as well as store information and have the ability to mutate. Nobody has been able to create such a cell. 

On the other hand, these scientific efforts actually point to a couple of conclusions: 

• That the digitally designed information that’s encoded into our DNA proves that life is much more than just chemistry and physics, with highly fine-tuned information on top controlling who we are. This information should come from intelligence. 

• That with the help of advanced computing and laboratories, existing purpose and knowledge, and existing life to copy from, it was still very hard to design and produce a functioning DNA, so how hard can it be to imagine that these complex systems were created on their own just by random or unguided natural processes with no tools or intention to create living organisms. 

If you want to read more about faith, science and evolution, check: Darwin and the Origin of Life

What Is Life

Introduction: 

Has Darwinian evolution explained how life came into existence? Were scientists able to create a synthetic form of life from non-living things, like simple bacteria for example? Were scientists able to create DNA or RNA? Were scientists able to create required organic molecules in replicating the prebiotic earth conditions? Was science able to explain the origin of life? Was it formed in primordial soup, in mud, in hydrothermal vents or was it formed somewhere else in outer space and landed on earth? 

One may think that science has already answered all these questions, or almost about to answer them all. The truth is that despite all scientific efforts on studying the origin of life for more than 70 years, nothing remarkable was achieved. All findings are still just hypotheses, and due to new scientific discoveries over these years, the knowledge gap increased, making it more difficult to come closer to answers. 

In this series of articles we will discuss the above questions, and describe the relevant scientific achievements and arguments about the origin of life. 

Life definition: 

Before talking about the origin of life, it might be interesting to define first: what’s life? 

Wikipedia describes life as: 

“… a characteristic that distinguishes physical entities that have biological processes, from those that do not, either because such functions have ceased (they have died) or because they never had such functions and are classified as non-living. 

Various forms of life exist, such as plants, animals, fungi, protists, archaea, and bacteria. 

There is currently no agreement regarding the definition of life. One popular definition is that organisms are open systems that maintain homeostasis (stable state), are composed of cells, have a life cycle, undergo metabolism, can grow, adapt to their environment, respond to stimuli, reproduce and evolve. Other definitions sometimes include non-cellular life forms such as viruses. 

NASA adopted an abstracted definition to identify extraterrestrial life as “a self-sustained chemical system capable of undergoing Darwinian evolution”. 

However, these definitions mainly focus on the characteristics of a living organism, not what life really is. 

Atheist scientists have also struggled to settle on a definition of life. In one of the debates about the definition of life, famous atheist scientists such as Richard Dawkins and Craig Venter avoided defining what life is, assuming they can search for other forms of life, or study the origin of life without defining it. 

Notably, they clearly stated many times during the debate that they simply “don’t know” the definition of life, and that science is so far away from explaining the origin of life. That debate also shows great disagreement within the scientific community on the origin of life, as some of them were optimistic that they would solve the mystery within 20 – 30 years, while others were sure that we will never be able to solve such a mystery. 

So how can we discuss the origin of something if we don’t know what that thing is in the first place?  

Materialistic point of view: 

Materialists always try to define everything through physics and chemistry, defining living things as molecules, abstracting life as chemicals that perform biological processes. So their main assumption is that if we were able to recreate or fabricate the chemistry required for life, the molecular building blocks, then life can evolve accordingly, having life from non-life. 

This assumption is facing a lot of difficulties: 

1. Ignoring a lot of non-materialistic aspects about life that need explanation, like: emotions, morals, consciousness, imagination, arts, intelligence, language, etc. While chemicals and molecules are required for life as the hardware, life is surely something on-top. Nothing convincing was presented so far to explain how these aspects evolved from chemical reactions.  

2. Producing organic life from non-organic chemistry has been extremely difficult and since the Miller–Urey experiment in1952, and after 70 years, results are still extremely far from achieving any remarkable success. 

3. Identifying the real prebiotic (early earth) conditions to try to replicate the chemistry of life, as evidence for the origin of life hypothesis. 

4. Identifying the basic form of life, i.e. what’s the minimum required abstraction of the living cell to declare that we have a living organism? 

5. If we successfully created all the organic life chemistry, how to put them together in a physical setup? And how was all that done by its own, in a purely unguided unconscious process, just by chance and time? 

6. Assuming we have an already formed fully functional cell, that just died, so all the chemistry and physics are in place, how to revive that dead cell and make it “live” again?  

Details about these points will be covered in the following arguments 

The car argument: 

Imagine a new car, coming in small pieces spread apart, unordered, thousands of different pieces, with you having no tools at all, no experience, no previous info of what these parts will produce at the end, and now you should start producing a meaningful thing that will turn out to be a car.  

What if even these parts were not all in your garage, but some parts are in volcanoes, others in oceans, others buried in the earth, others are so rare to find, and you don’t even know that you will need them?  

What if also that car should be self-maintaining, like driving on its own, or getting its own fuel with no software installed?  

What about corrosion that might impact these parts before you successfully finish the task? 

Do you think you will be able to produce that car ever? Although this task seems to be so difficult, it’s still much easier than what materialists are assuming to just happen coincidentally to form the living cell. 

Other Scientific point of view: 

A lot of scientists are not convinced with the materialistic point of view about the definition of life and the origin of life. 

One example is Paul Davies – an agnostic scientist – who explained in one of his lectures (reference 3), his vision about biology as: Information! that it is all about coding, signals, and instructions, while physics/chemistry is about matter, force, and energy, stating that life is surely more than just chemistry and physics. He also stated that to be able to answer “How” life originated, we need to answer these questions first about: 

1. How software emerges from hardware 

2. How non-trivial programmable constructions emerge from “dumb molecules” 

3. How digital information storage and processing emerge from analog information 

4. How instructional or contextual information emerge from “mere bits” (Shannon information) 

5. How top-down information flow emerges from bottom-up information flow 

Other scientists such as John Lennox, and Stephen Meyer used that analogy of software and hardware many times, and how cells are full of information, and since information can’t be generated on its own unless invoked by an external intelligent agent, then there must be an intelligent designer who encoded the living cells.  

Christian point of view: 

According to Christian belief, we believe that God created all living organisms, and that God is the source of life, and is Life itself. Therefore, life has no meaning without God. 

In him was life (John1:4) 

Jesus answered, “I am the way and the truth and the life. (John 14: 6) 

Also the book of Acts spoke about Jesus as “the author of life” (Acts 3: 15) 

We don’t know how God created all living organisms, but the general blueprint in Genesis 1 clearly stated that God blessed the living creatures to be fruitful and to increase in number.  

• Then God said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.” And it was so. 
• And God said, “Let the water teem with living creatures, and let birds fly above the earth across the vault of the sky.” … God blessed them and said, “Be fruitful and increase in number and fill the water in the seas, and let the birds increase on the earth.” 
• And God said, “Let the land produce living creatures according to their kinds: the livestock, the creatures that move along the ground, and the wild animals, each according to its kind.” And it was so. 
• So God created mankind in his own image, in the image of God he created them; male and female he created them. God blessed them and said to them, “Be fruitful and increase in number; fill the earth and subdue it. Rule over the fish in the sea and the birds in the sky and over every living creature that moves on the ground.” 

What if scientists succeed in producing living organisms from nonliving matter? 

The idea behind the materialistic point of view, is that if we are able to have life emerging from non-life, then there’s no need to have a God, and the argument used by religious people that God is the source of life will be rebutted accordingly. However, that would still be a logical fallacy because such an experiment, even if claimed that it mimics natural causes in prebiotic earth, is itself a “designed” experiment by intelligent humans.  

Next articles: 

In the following articles we shall cover: 

• The cell, the building block for life as we know it 

• Building blocks molecule 
• DNA, the life code 
• Micro-machinery 

• Synthetic Biology 

• Darwinian evolution and Origin of Life 
• Origin of Life different hypotheses  

• Prebiotic soup 
• hydrothermal vents  
• RNA world hypothesis 

• Chemical evolution 

• Synthetic Chemistry for life building blocks 
• Thermodynamics and energy conservation within cell formation 

Summary 

Life as per scientists consists of:  Material (Chemistry + Physics) + Information (instructions + coding + interactions+ ..)  

Scientists are still clueless about non-materialistic life aspects 

Scientists are still clueless about Origin of Life 

Source Life as per Christian faith is: God 

References: 

1 Definition of life: Life – Wikipedia 

2 The Great Debate – What is Life? – YouTube 

Richard Dawkins, J. Craig Venter, Nobel laureates Sidney Altman and Leland Hartwell, Chris McKay, Paul Davies, Lawrence Krauss, and The Science Network’s Roger Bingham discuss the origins of life, the possibility of finding life elsewhere, and the latest development in synthetic biology. 

3 Paul Davies – “The Origin of Life” (C4 Public Lecture) – YouTube 

4 Signature in the Cell: Stephen Meyer Faces his Critics, pt. 1: The Presentation – YouTube 

5 Stephen Meyer Debunks the “God of the Gaps” Objection – YouTube