F Rosa Rubicondior: Creationism in Crisis - The Evolution of Life and the Genetic Code.

Sunday 28 May 2023

Creationism in Crisis - The Evolution of Life and the Genetic Code.

Genetic information is stored as long, complex sequences of the four different bases in DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). Triplets of these bases are interpreted by the genetic machinery as instructions to add a certain amino acid to a protein.

Alfred Pasieka/Science Photo Library/Getty Images Plus
Did life evolve more than once? Researchers are closing in on an answer

By way of an introduction to this article on abiogenesis, I'm going to try to dispel the common, but evidence-free claim from creationists that the genetic code is so complex that it must have been designed by an intelligent designer.

This is, of course, nothing but the usual argument from ignorant incredulity and a false dichotomy fallacy - I don't know enough, I can't be bothered to learn, and I can't imagine how something could have arisen naturally, so God did it - and of course it must be the locally popular god because there are only two possibilities; the current science or the local god. It's an argument that demonstrates better than most the scientific illiteracy, intellectual bankruptcy and cultural chauvinism of creationism.

First, I look at the genetic codes and how it could have evolved naturally, without a supernatural magician making chemistry and physics do things they couldn't do without it, or making the highly improbable happen - as though the notion of an undetectable entity existing outside space and time but able to influence things inside space and time makes any sense.

This comes in two forms: a conversation with an AI chat bot, and the book, Life Ascending by Nick Lane.

Firstly, a conversation with ChatGPT3:
Q: What are the current theories on how the 'genetic code' evolved?
A: The origin and evolution of the genetic code is a fascinating topic in the field of molecular biology and evolutionary biology. While the exact details and mechanisms of how the genetic code emerged are still being studied and debated, there are several theories that attempt to explain its evolution. Here are some of the current theories:

  • The Stereochemical Theory: This theory suggests that the genetic code evolved through interactions between amino acids and their corresponding RNA molecules. It proposes that early in evolution, small RNA molecules acted as both catalysts (ribozymes) and carriers of genetic information. Over time, the interactions between amino acids and specific RNA molecules became more standardized, leading to the development of the genetic code.
  • The Coevolution Theory: According to this theory, the genetic code and the amino acids evolved together in a coevolutionary process. It proposes that early life forms synthesized amino acids based on available resources in their environment. As these amino acids accumulated, they drove the selection for specific codons in the genetic code that would correspond to those amino acids, creating a mutual dependency between the code and the amino acids.
  • The Frozen Accident Theory: This theory suggests that the genetic code evolved randomly and that its specific characteristics are a result of historical accidents. According to this theory, the genetic code could have initially been more flexible and allowed for different codon-amino acid assignments. However, once a particular code became established in early life forms, it remained relatively fixed due to the high cost and potential errors associated with changing the code.
  • The RNA World Hypothesis: This hypothesis proposes that early life forms relied solely on RNA for both information storage and enzymatic functions. In this scenario, the genetic code could have emerged from the interactions between RNA molecules and amino acids. As more complex molecules, such as proteins, became essential for cellular processes, the genetic code evolved to encode the synthesis of these molecules.
It's important to note that these theories are not mutually exclusive, and elements from multiple theories may contribute to our understanding of how the genetic code evolved. The field of research is dynamic, and new findings and insights continue to shape our understanding of this intriguing phenomenon.

Q: Is there any general relationship between the bases in a codon and the amino acid they code for?
A: Yes, there is a relationship between the bases in a codon and the amino acid they code for. The genetic code is a set of rules that specifies the correspondence between a sequence of three nucleotides (codon) in mRNA and a specific amino acid or a stop signal. The genetic code is degenerate, meaning that multiple codons can code for the same amino acid.

The genetic code is composed of 64 possible codons, of which 61 code for amino acids, and the remaining three (UAA, UAG, and UGA) serve as stop codons, indicating the end of protein synthesis. The correspondence between codons and amino acids is almost universal across living organisms, although some exceptions and variations exist.

The relationship between codons and the amino acids they encode is based on the specific sequence of nucleotides in the codon. Each codon consists of three consecutive bases (A, U, G, or C). For example, the codon "AUG" codes for the amino acid methionine, which typically serves as the start codon for protein synthesis.

The relationships between codons and amino acids are established through the interactions between tRNA molecules and the codons in mRNA during protein synthesis. Each amino acid is attached to a specific type of transfer RNA (tRNA) molecule, which contains an anticodon region that is complementary to the codon in mRNA. The anticodon of the tRNA molecule base-pairs with the corresponding codon in mRNA, allowing the specific amino acid to be incorporated into the growing protein chain.

It's important to note that while some amino acids are encoded by a single codon (e.g., methionine by AUG), most amino acids have multiple codons that can code for them due to the degeneracy of the genetic code. For example, the amino acid leucine is specified by six different codons: UUA, UUG, CUU, CUC, CUA, and CUG.

Overall, the relationship between the bases in a codon and the amino acid they code for is established through the genetic code, and it is crucial for the accurate translation of genetic information into functional proteins.

Q: With leucine the central base of the RNA codon is uracil. Is that significant or just a coincidence?
A: The fact that the central base in the RNA codons for leucine is uracil (U) is not merely a coincidence. It is a significant feature of the genetic code that has been shaped by evolutionary processes. The relationship between the central base of the codon and the amino acid it codes for is not fully understood, but it is believed to have arisen through evolutionary selection pressures.

The genetic code has evolved in a way that minimizes errors in protein synthesis caused by mutations or changes in the DNA sequence. This includes avoiding potential errors that could arise from base substitutions or mutations in the genetic code itself. It is thought that the particular arrangement of bases in the codons may have been selected to reduce the likelihood of such errors occurring.

In the case of leucine, the codons that code for this amino acid (UUA, UUG, CUU, CUC, CUA, CUG) all have uracil (U) as the central base. This arrangement may provide a certain level of redundancy and error tolerance. For example, if a mutation were to occur that changed the central base from uracil to another base, it would likely result in a codon that still codes for leucine due to the degeneracy of the genetic code. This redundancy helps to ensure the fidelity of protein synthesis even in the presence of mutations.

The specific reasons for why uracil is consistently found in the central position of the leucine codons are still a subject of scientific investigation. It is likely that multiple factors, including the chemical properties of the bases, the interactions between tRNA and mRNA molecules, and the historical constraints of the genetic code, have contributed to this arrangement.

Which is broadly in line with the following detailed explanation of how the genetic code evolved, by Nick Lane:
It’s only when we see the code as the product of biosynthesis – the product of cells capable of making their own building blocks from hydrogen and carbon dioxide – that the patterns begin to make sense.

So what are these elusive patterns? A different pattern is linked with each letter of the triplet code. The first letter is the most striking, for it is associated with the steps that turn a simple precursor into an amino acid. The principle is so startling that it’s worth spelling out briefly. In cells today, amino acids are made via a series of biochemical steps, starting from several different simple precursors. The surprising observation is that there is a tie between the first letter of the triplet codon and these simple precursors. Thus, all amino acids formed from the precursor pyruvate share the same first letter in the codon – T in this case. 5I use the example of pyruvate because it is a molecule that we have already met in Chapter 1. It can be formed in hydrothermal vents from carbon dioxide and hydrogen, catalysed by minerals found in the vents. But pyruvate is not alone in this regard. All the amino acid precursors are part of the core biochemistry of all cells, the Krebs cycle, and should form in the type of hydrothermal vent discussed in Chapter 1. The implication, admittedly weak at this point but set to deepen, is that there is a link between hydrothermal vents and the first position of the triplet code.

What about the second letter? Here the association is with the degree to which an amino acid is soluble or insoluble in water, which is to say, its hydro-phobicity. Hydrophilic amino acids dissolve in water, whereas hydrophobic amino acids are immiscible, dissolving in fats or oils such as the lipid membranes of cells. The amino acids can be sorted into a spectrum, running from ‘very hydrophobic’ to ‘very hydrophilic’, and it’s this spectrum that bears a relationship with the second position of the triplet code. Five of the six most hydrophobic amino acids have T as the middle base, whereas all the most hydrophilic have A. The intermediates have a G or a C. Overall, then, there are strong deterministic relationships between the first two positions of every codon and the amino acid encoded, for whatever reasons.

The final letter is where the degeneracy lies, with eight amino acids having (a lovely technical term, this) fourfold degeneracy. While most people might picture a fourfold degenerate as a staggering drunkard, who manages to collapse into four different gutters, biochemists merely mean that the third position of the codon is information-free: it doesn’t matter which base is present, as all four possibilities encode the same amino acid. In the case of glycine, encoded by the triplet GGG, for example, the final G can be switched to a T, A or C – each triplet still codes for glycine. The degeneracy of the code in the third position has several interesting implications. We ’ve already noted that a doublet code could encode up to 16 out of the 20 different amino acids. If we eliminate the 5 most complex amino acids (leaving 15, plus a stop codon), the patterns in the first two letters of the code become even stronger. It might be, then, that the primordial code was a doublet, and was only later expanded into a triplet code, by ‘codon capture ’; the amino acids competed among themselves for the third position. If so, the earliest amino acids may have had an ‘unfair’ advantage in ‘taking over’ triplet codons, and this seems to be true. For example, the 15 amino acids most likely to have been encoded by the early doublet code hog between them 53 out of 64 possible triplets, an average of 3.5 codons per amino acid. In contrast, the 5 ‘later’ additions muster only 8 codons between them, an average of just 1. 6. It certainly looks like the early birds got the worms.

So let’s entertain the possibility that the code was initially a doublet, not a triplet, encoding a total of 15 amino acids (plus one ‘stop’ codon). This early code seems to have been almost entirely deterministic, which is to say that it was dictated by physical and chemical factors. There are few exceptions to the rules that the first letter is allied to the precursor, while the second letter is linked to the hydrophobicity of the amino acid. There is little scope here for any play of chance, no freedom from the physical rules.

But the third letter is a different matter. Here, with so much flexibility, there could have been a play of chance, and with that it became possible for selection to ‘optimise ’ the code. This, at any rate, was the radical proposition of two English molecular biologists, Lawrence Hurst and Stephen Freeland, in the late 1990s. The pair made science headlines when they compared the genetic code with millions of random computer-generated codes. They considered the damage that could be done by point mutations, in which one letter of a codon is switched for another. Which code, they wondered, could resist such point mutations best, either by retaining exactly the same amino acid, or by substituting a similar one? They found that the real genetic code is startlingly resistant to change: point mutations often preserve the amino acid sequence, and if a change does occur, a physically related amino acid tends to be substituted. In fact, Hurst and Freeland declared the genetic code to be better than a million alternative randomly generated codes. Far from being the folly of nature ’s blind cryptographer, the code is one in a million. Not only does it resist change, they say, but also by restricting the catastrophic consequences of the changes that do occur, the code actually speeds up evolution: obviously, mutations are more likely to be beneficial if they are not catastrophic.

Short of positing celestial design, the only way to explain optimisation is via the workings of selection. If so, the code of life must have evolved. Certainly, a number of trivial variations in the ‘universal’ code among bacteria and mitochondria do show that, if nothing else, the code can evolve, at least under exceptional circumstances. But how does it change without causing mayhem, you may ask, with Crick? The answer is: discretely. If an amino acid is encoded by four or even six different codons, some tend to be used more often than others. The rarely used codons can in practice be redesignated to a different (but probably related) amino acid without catastrophic consequences. And so the code evolves.

Altogether, then, the ‘code within the codons’ speaks of a physical process, initially related to the biosynthesis and solubility of amino acids, followed later by expansion and optimisation.
Lane, Nick. Life Ascending (pp. 46-49). (Kindle Edition.)
Will any creationist read this, and if any do, will they understand it?

You can bet your house that the same old 'The genetic code proves intelligent design' argument will still be around for the foreseeable future because the last thing any creationist wants is scientific evidence that they're wrong.

So now to the article by Jordi Paps, a senior lecturer in the School of Biological Sciences, University of Bristol, Bristol UK. The article is reproduced from The Conversation under a Creative Commons license, reformatted for stylistic consistency:

Did life evolve more than once? Researchers are closing in on an answer

Jordi Paps, University of Bristol

From its humble origin(s), life has infected the entire planet with endless beautiful forms. The genesis of life is the oldest biological event, so old that no clear evidence was left behind other than the existence of life itself. This leaves many questions open, and one of the most tantalising is how many times life magically emerged from non-living elements.

Has all of life on Earth evolved only once, or are different living beings cut from different cloths? The question of how difficult it is for life to emerge is interesting – not least because it can shed some light on the likelihood of finding life on other planets.

The origin of life is a central question in modern biology, and probably the hardest to study. This event took place four billion years ago, and it happened at a molecular level – meaning little fossil evidence remains.

Many lively beginnings have been suggested, from unsavoury primordial soups to outer space. But the current scientific consensus is that life emerged from non-living molecules in a natural process called abiogenesis, most likely in the darkness of deep-sea hydrothermal vents. But if life emerged once, why not more times?

What is abiogenesis?

Scientists have proposed various consecutive steps for abiogenesis. We know that Earth was rich in several chemicals, such as amino acids, a type of molecules called nucleotides or sugars, which are the building blocks of life. Laboratory experiments, such as the iconic Miller-Urey experiment, have shown how these compounds can be naturally formed under conditions similar to early Earth. Some of these compounds could also have come to Earth riding meteorites.
Smoking hydrothermal vent.
Smoking hydrothermal vent.
Source: NOAA/wikipedia.
Next, these simple molecules combined to form more complex ones, such as fats, proteins or nucleic acids. Importantly, nucleic acids — such as double-stranded DNA or its single-stranded cousin RNA — can store the information needed to build other molecules. DNA is more stable than RNA, but in contrast, RNA can be part of chemical reactions in which a compound makes copies of itself – self-replication.

The “RNA world” hypothesis suggests that early life may have used RNA as material for both genes and replication before the emergence of DNA and proteins.

Once an information system can make copies of itself, natural selection kicks in. Some of the new copies of these molecules (which some would call “genes”) will have errors, or mutations, and some of these new mutations will improve the replication ability of the molecules. Therefore, over time, there will be more copies of these mutants than other molecules, some of which will accumulate further new mutations making them even faster and more abundant, and so on.

Eventually, these molecules probably evolved a lipid (fatty) boundary separating the internal environment of the organism from the exterior, forming protocells. Protocells could concentrate and organise better the molecules needed in biochemical reactions, providing a contained and efficient metabolism.

Life on repeat?

Abiogenesis could have happened more than once. Earth could have birthed self-replicating molecules several times, and maybe early life for thousands or millions of years just consisted of a bunch of different self-replicating RNA molecules, with independent origins, competing for the same building blocks. Alas, due to the ancient and microscopic nature of this process, we may never know.

Many lab experiments have successfully reproduced different stages of abiogenesis, proving they could happen more than once, but we have no certainty of these occurring in the past.

A related question could be whether new life is emerging by abiogenesis as you are reading this. This is very unlikely though. Early Earth was sterile of life and the physical and chemical conditions were very different. Nowadays, if somewhere on the planet there were ideal conditions for new self-replicating molecules to appear, they would be promptly chomped by existing life.

What we do know is that all extant life beings descend from a single shared last universal common ancestor of life (also known as LUCA). If there were other ancestors, they left no descendants behind. Key pieces of evidence support the existence of LUCA. All life on Earth uses the same genetic code, namely the correspondence between nucleotides in DNA known as A, T, C, and G – and the amino acid they encode in proteins. For example, the sequence of the three nucleotides ATG always corresponds to the amino acid methionine.

Theoretically, however, there could have been more genetic code variants between species. But all life on Earth uses the same code with a few minor changes in some lineages. Biochemical pathways, such as the ones used to metabolise food, also support the existence of LUCA; many independent pathways could have evolved in different ancestors, yet some (such as the ones used to metabolise sugars) are shared across all living organisms. Similarly, hundreds of identical genes are present in disparate live beings which can only be explained by being inherited from LUCA.
Image of a chimp holding its ears.
Just like us…
My favourite support for LUCA comes from the Tree of Life. Independent analyses, some using anatomy, metabolism or genetic sequences, have revealed a hierarchical pattern of relatedness that can be represented as a tree. This shows we are more related to chimps than to any other living organisms on Earth. Chimps and we are more related to gorillas, and together to orangutans, and so on.

You can pick any random organism, from the lettuce in your salad to the bacteria in your bioactive yogurt and, if you travel back in time far enough, you will share an actual common ancestor. This is not a metaphor, but a scientific fact.

This is one of the most mind boggling concepts in science, Darwin’s unity of life. If you are reading this text, you are here thanks to an uninterrupted chain of reproductive events going back billions of years. As exciting as it is to think about life repeatedly emerging on our planet, or elsewhere, it is even more exciting to know that we are related to all the life beings in the planet. The Conversation
Jordi Paps, Senior lecturer, School of Biological Sciences, University of Bristol, University of Bristol

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Published by The Conversation.
Open access. (CC BY 4.0)
And lastly, to complete the picture, here is the ten-steps to abiogenesis I outlined in my book, What Makes You So Special: From the Big Bang to You, based on the work of Nick Lane and Michael Le Page in New Scientist:
The honest answer to this question [How did the first living organisms arise?], like the question of how the first simple self–replicating molecule arose and what it was, is that we do not yet know. We do not know if it was a single line of development or two or more that later got together. However, laboratory experiments have come up with a very plausible series of steps, as outlined in a New Scientist article by Nick Lane and Michael Le Page (Lane & Le Page, 2009). They assumed that the most likely location for it to have happened was in porous rocks in alkaline waters around geothermal vents and outlined ten steps:
  1. Water filtering down into newly–formed rocks around geothermal vents reacted with minerals to produce an alkaline, hydrogen and sulphide rich fluid that welled up in the vents.
  2. This fluid reacted with acidic sea water which was then rich in iron to form deposits of highly porous carbonate rock and a foam of iron–sulphur bubbles.
  3. Hydrogen and carbon dioxide trapped in these bubbles reacted to make simple organic molecules such as methane, formates and acetates; reactions that would have been catalysed by iron–sulphur compounds.
  4. The electrochemical gradient between the alkaline fluid in the pores and the acidic seawater would have provided energy to drive the spontaneous formation of acetyl phosphate and pyrophosphate. These behave like ATP (adenosine triphosphate) which powers modern cells. This power supply would in turn power the formation of amino acids and nucleotides.
  5. Currents produced by thermal gradients and diffusion within the porous carbonate rock would have concentrated the larger molecules creating the conditions for building RNA, DNA and proteins and creating the conditions for an evolutionary process where molecules that could catalyse the formation of copies of themselves would quickly dominate and win the struggle for resources.
  6. Fatty molecules would have coated the surface of the pores in the rock, enclosing the self–replicating molecules in a primitive cell membrane.
  7. Eventually, the formation of the protein catalyst, pyrophosphatase enabled the protocell to extract more energy from the acid–alkaline gradient. This enzyme is still found in some bacteria and archaea.
  8. Some protocells would have started using ATP as their primary energy source, especially with the formation of the enzyme ATP synthase. This enzyme is common to all life today.
  9. Protocells in locations where the electrochemical gradient was weak could have generated their own gradient by pumping protons across their membrane using the energy released by the reaction between hydrogen and carbon dioxide, so producing a sufficient gradient to power the formation of ATP.
  10. The ability to generate their own chemical gradient freed these protocells from dependence on the pores in the rock, so they were now free to become free–living cells. This could have happened at least twice with slightly different cells, one type giving rise to bacteria; the other to archaea.
The above ten–step process is of course speculative and probably impossible to test and verify in a laboratory because the conditions around these geothermal vents deep below the ocean would be impossible to replicate in a laboratory, as would the time it might have taken. No–one is claiming it all happened in a day or two, or even weeks or years; not even the lifetime of a working scientist. It could have taken tens or hundreds of millions of years. No–one was in any hurry and there was no objective. Things happened when they happened.

Does anyone think any of that will stop creationists false witnessing against science by claiming science can't explain the origins of life or the genetic code?

Without their self-licensed exemption from the commandments not to bear false witness, and not to be hypocrites, where would creationism be? Exactly where they are today - ignorant, intellectually and morally bankrupt fools led by self-aggrandizing frauds.

Thank you for sharing!

submit to reddit

No comments :

Post a Comment

Obscene, threatening or obnoxious messages, preaching, abuse and spam will be removed, as will anything by known Internet trolls and stalkers, by known sock-puppet accounts and anything not connected with the post,

A claim made without evidence can be dismissed without evidence. Remember: your opinion is not an established fact unless corroborated.

Web Analytics