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New study: the early Earth’s atmosphere contained oxygen

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Here’s a new paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”.

Evolution News explains what the paper is about.

Excerpt:

A recent Nature publication reports a new technique for measuring the oxygen levels in Earth’s atmosphere some 4.4 billion years ago. The authors found that by studying cerium oxidation states in zircon, a compound formed from volcanic magma, they could ascertain the oxidation levels in the early earth. Their findings suggest that the early Earth’s oxygen levels were very close to current levels.

[…]Miller and Urey conducted experiments to show that under certain atmospheric conditions and with the right kind of electrical charge, several amino acids could form from inorganic compounds such as methane, ammonia, and water. Several experiments have been done using various inorganic starting materials, all yielding a few amino acids; however, one key aspect of all of these experiments was the lack of oxygen.

If the atmosphere has oxygen (or other oxidants) in it, then it is an oxidizing atmosphere. If the atmosphere lacks oxygen, then it is either inert or a reducing atmosphere. Think of a metal that has been left outside, maybe a piece of iron. That metal will eventually rust. Rusting is the result of the metal being oxidized. With organic reactions, such as the ones that produce amino acids, it is very important that no oxygen be present, or it will quench the reaction. Scientists, therefore, concluded that the early Earth must have been a reducing environment when life first formed (or the building blocks of life first formed) because that was the best environment for producing amino acids. The atmosphere eventually accumulated oxygen, but life did not form in an oxidative environment.

The problem with this hypothesis is that it is based on the assumption that organic life must have formed from inorganic materials. That is why the early Earth must have been a reducing atmosphere. Research has been accumulating for more than thirty years, however, suggesting that the early Earth likely did have oxygen present.

[…]This brings us back to that Nature letter, which offers another reason to question the reducing environment of the early Earth. The authors looked at the cerium oxidation levels within zircon. Zircon is a hard rock that forms from the solidification of magma. Several studies have been done with zircon because of its age and durability. (See here for a report on using zircon to determine when oceans and land were present on Earth.) Cerium (Ce) is an element that can be found in early Earth zircon. The ratio of cerium’s +3 and +4 oxidation states indicates the environmental conditions at the time the cerium was trapped in the zircon. Specifically, cerium’s oxidation ratio is related to the amount of oxygen in the atmosphere. The authors created cerium-infused zircon in the lab at various oxidative ratios to make a calibration curve to which they could then compare the early Earth samples.

Their findings not only showed that oxygen was present in the early Earth atmosphere, something that has been shown in other studies, but that oxygen was present as early as 4.4 billion years ago. This takes the window of time available for life to have begun, by an origin-of-life scenario like the RNA-first world, and reduces it to an incredibly short amount of time. Several factors need to coincide in order for nucleotides or amino acids to form from purely naturalistic circumstances (chance and chemistry). The specific conditions required already made purely naturalist origin-of-life scenarios highly unlikely. Drastically reducing the amount of time available, adding that to the other conditions needing to be fulfilled, makes the RNA world hypothesis or a Miller-Urey-like synthesis of amino acids simply impossible.

So here’s where we stand. If you are a materialist, then you need a reducing environment on the early Earth in order to get organic building blocks (amino acids) from inorganic materials. However, the production of these organic building blocks (amino acids) requires that the early Earth atmosphere be oxygen-free. And the problem with this new research, which confirms previous research, is that the early Earth contained huge amounts of oxygen – the same amount of oxygen as we have today. This is lethal to naturalistic scenarios for creating the building blocks of life on the Earth’s surface.

Other problems

If you would like to read a helpful overview of the problems with a naturalistic scenario for the origin of life, check out this article by Casey Luskin.

Excerpt:

The “origin of life” (OOL) is best described as the chemical and physical processes that brought into existence the first self-replicating molecule. It differs from the “evolution of life” because Darwinian evolution employs mutation and natural selection to change organisms, which requires reproduction. Since there was no reproduction before the first life, no “mutation – selection” mechanism was operating to build complexity. Hence, OOL theories cannot rely upon natural selection to increase complexity and must create the first life using only the laws of chemistry and physics.

There are so many problems with purely natural explanations for the chemical origin of life on earth that many scientists have already abandoned all hopes that life had a natural origin on earth. Skeptical scientists include Francis Crick (solved the 3-dimensional structure of DNA1) and Fred Hoyle (famous British cosmologist and mathematician), who, in an attempt to retain their atheistic worldviews, then propose outrageously untestable cosmological models or easily falsifiable extra-terrestrial-origin-of-life / panspermia scenarios2 which still do not account for the natural origin of life. So drastic is the evidence that Scientific American editor John Horgan wrote, “[i]f I were a creationist, I would cease attacking the theory of evolution … and focus instead on the origin of life. This is by far the weakest strut of the chassis of modern biology.”3

The article goes over the standard problems with naturalistic scenarios of the origin of life: wrong atmosphere, harmful UV radiation, interfering cross-reactions, molecular oxygen, meteorite impacts, chirality, etc.

Charles Thaxton explains the origin of life

Here’s a helpful little video on the problem from origin of life chemist Charles Thaxton, who authored “The Mystery of Life’s Origin” with Walter Bradley and Roger Olsen.

There’s another video like this one featuring Dean Kenyon, and you can get the video clips online here. I really wish someone would post it online. I have the video and ripped it from my VHS tape, so maybe I should do it! It’s a great interview. Both of these videos (Thaxton, Kenyon) are highly recommended for intermediate and advanced Christians. For beginners, I would recommed “Unlocking the Mystery of Life”, which you can watch for free right here:

If you are looking for a hot issue to put some time into, then this is a good place to start. And note that this problem of the building blocks of life is logically prior to the problem of forming functional sequences of amino acids (e.g. – proteins), which people like Stephen C. Meyer debate about. In debates on the origin of life, ID people usually just assume that the amino acids exist, and then get on with discussing the problem of generating sequences of amino acids and base pairs into sequences that exhibit specified complexity. But as you see from the research, it’s an unwarranted assumption – those building blocks are not a given, and the naturalist has to account for them.

Polemics

Can naturalism account for the origin of the 20 amino acids in living systems?

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The origin of life

There are two problems related to the origin of the first living cell, on atheism:

  1. The problem of getting the building blocks needed to create life – i.e. the amino acids
  2. The problem of creating the functional sequences of amino acids and proteins that can support the minimal operations of a simple living cell

Normally, I concede the first problem and grant the atheist all the building blocks he needs. This is because step 2 is impossible. There is no way, on atheism, to form the sequences of amino acids that will fold up into proteins, and then to form the sequences of proteins that can be used to form everything else in the cell, including the DNA itself. But that’s tomorrow’s topic.

Today, let’s take a look at the problems with step 1.

The problem of getting the building blocks of life

Now you may have heard that some scientists managed to spark some gasses to generate most of the 20 amino acids found in living systems. These experiments are called the “Miller-Urey” experiments.

The IDEA center has a nice summary of origin-of-life research that explains a few of the main problems with step 1.

Miler and Urey used the wrong gasses:

Miller’s experiment requires a reducing methane and ammonia atmosphere,11, 12 however geochemical evidence says the atmosphere was hydrogen, water, and carbon dioxide (non-reducing).15, 16 The only amino acid produced in a such an atmosphere is glycine (and only when the hydrogen content is unreasonably high), and could not form the necessary building blocks of life.11

Miller and Urey didn’t account for UV of molecular instability:

Not only would UV radiation destroy any molecules that were made, but their own short lifespans would also greatly limit their numbers. For example, at 100ºC (boiling point of water), the half lives of the nucleic acids Adenine and Guanine are 1 year, uracil is 12 years, and cytozine is 19 days20 (nucleic acids and other important proteins such as chlorophyll and hemoglobin have never been synthesized in origin-of-life type experiments19).

Miller and Urey didn’t account for molecular oxygen:

We all have know ozone in the upper atmosphere protects life from harmful UV radiation. However, ozone is composed of oxygen which is the very gas that Stanley Miller-type experiments avoided, for it prevents the synthesis of organic molecules like the ones obtained from the experiments! Pre-biotic synthesis is in a “damned if you do, damned if you don’t” scenario. The chemistry does not work if there is oxygen because the atmosphere would be non-reducing, but if there is no UV-light-blocking oxygen (i.e. ozone – O3) in the atmosphere, the amino acids would be quickly destroyed by extremely high amounts of UV light (which would have been 100 times stronger than today on the early earth).20, 21, 22 This radiation could destroy methane within a few tens of years,23 and atmospheric ammonia within 30,000 years.15

And there were three other problems too:

At best the processes would likely create a dilute “thin soup,”24 destroyed by meteorite impacts every 10 million years.20, 25 This severely limits the time available to create pre-biotic chemicals and allow for the OOL.

Chemically speaking, life uses only “left-handed” (“L”) amino acids and “right-handed” (“R)” genetic molecules. This is called “chirality,” and any account of the origin of life must somehow explain the origin of chirality. Nearly all chemical reactions produce “racemic” mixtures–mixtures with products that are 50% L and 50% R.

Two more problems are not mentioned in the article. A non-peptide bond anywhere in the chain will ruin the chain. You need around 200 amino acids to make a protein. If any of the bonds is not a peptide bond, the chain will not work in a living system. Additionally, the article does not mention the need for the experimenter to intervene in order to prevent interfering cross-reactions that would prevent the amino acids from forming.

Usually when you hear the origin of life debated, they sort of skirt about the problem of where the amino acids come from, but there is no reason not to make that an issue. The naturalist has to explain how the first living cell could come about naturalistically.

Further study

One of my favorite resources on the origin of life is this interview from the University of California with former atheist and origin of life researcher Dean Kenyon. Kenyon, a professor of Biology at San Francisco State University, wrote the textbook on “chemical evolution”, which is the view that chemicals can arrange themselves in order to create the first living cell, without intervention.

This interview from the University of California with another origin of life researcher, Charles Thaxton, is also one of my favorites.

You’ll need Quicktime to see the videos, or buy the videos from ARN. (Kenyon, Thaxton) I have both of them – they rock!

Polemics

The origin of life, part 2 of 2: biological information

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Last time we saw how the progress of science in the last 30 years has proved that the environment of the early Earth would not have allowed the emergence of the basic building blocks of life. This time, let’s allow the atheist to assume the building blocks were created by the noodly appendage of the Flying Spaghetti Monster, (peas be upon him), and see whether it’s possible for the blocks to chain themselves together to make a living cell withinin a reasonable amount of time (400 million years, say).

For this post, I will be referencing an article by Stephen C. Meyer, which he published in the Catholic journal “First Things”. I chose this article deliberately because it was written at the level of an ordinary layman, so we could all understand everything well enough to feel confident explaining it to our neighbors. All unattributed quotes are from this article.

The combatants

The contest over origins features two opposing points of view:

  • A Creator and Designer is responsible for the origin of life
  • Matter, chance and long periods of time are sufficient to explain the origin of life

What’s at stake?

Atheistic Cornell University professor Will Provine explains what logically follows from naturalistic evolution:

There are no gods, no purposes, and no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end of me. There is no ultimate foundation for ethics, no ultimate meaning in life, and no free will for humans, either. What an unintelligible idea.

So, the stakes are high.

Why doubt the apparent design in nature?

There are two main reasons why atheists doubt the appearance of design in nature:

Minimal life functionality requires information

In order for a living organism to support life, it must be able to perform minimal functions:

  • store information
  • transmit information
  • edit information
  • use that information to regulate metabolic processes

There must be sufficient information inside the cells of that organism to support those functions. How does this information exist in the cell, and where did it come from?

Atheism is a pre-scientific worldview

Meyer describes the primitive superstitions of tribes of atheists living in primitive, pre-scientific cultures:

…in the 1870s and 1880s scientists assumed that devising an explanation for the origin of life would be fairly easy….they assumed that life was essentially a rather simple substance called protoplasm that could be easily constructed by combining and recombining simple chemicals such as carbon dioxide, oxygen, and nitrogen. …just as salt could be produced spontaneously by adding sodium to chloride, so… could a living cell be produced by adding together several chemical constituents and then allowing spontaneous chemical reactions to produce the simple protoplasmic substance that they assumed to be the essence of life.

Atheists believe in all kinds of primitive pre-scientific myths, like the eternal universe, etc., which the progress of science has falsified. Can the progress of science falsify the atheistic superstitions about the origin of life?

The Oparin-Haldane hypothesis

Atheists began to panic in the early 20th century as discoveries began to pile up confirming the that the entire physical universe, and time itself, was created by a supernatural force that existed transcendentally, independent of matter, energy, space and time. (See here for a listing of 6 of these discoveries from the progress of science). Atheists decided that they’d better get involved in this “science” thing that the Christians had started.

Meyer reports on one of their first groundless speculations:

During the 1920s and 1930s a more sophisticated version of this so–called “chemical evolutionary theory” was proposed by a Russian biochemist named Alexander I. Oparin…. Oparin, like his nineteenth–century predecessors, suggested that life could have first evolved as the result of a series of chemical reactions.

It was hoped that that the Flying Spaghetti Monster would appear to his true believers and ground this blind speculation, allowing atheists to continue in their flight from rationality and moral obligations.

The Miller-Urey experiment

Pre-biotic synthesis (see below) produces amino acids, which are the first step in explaining the origin of the simplest life, on atheism:

How did life begin?
How did life begin?

As we saw last time, the Miller-Urey experiments that were designed to produce the building blocks of life (amino acids) were horribly flawed and did not reflect the conditions that would have existed on the early Earth.

I’ll summarize the problems with the experiment:

  • the gasses were used in the experiment were not those present on the early Earth
  • molecular oxygen was excluded from the experiment
  • Harmful UV radiation was filtered out by the experimenter intervention
  • interfering cross-reactions were prevented by experimenter intervention

Other problems:

  • extinction events, such as meteorite impacts, were excluded not considered
  • the chirality problem (left-handed amino acids, right-handed sugars) was not considered
  • the problem of getting all peptide bonds was not considered

This experiment, though flawed, still exists in biology textbooks today, along side faked photographs of peppered moths and doctored drawings of embryos. All must praise the Flying Spaghetti Monster, and at taxpayer expense!

The problem of biological information

To create life, you need to sequence amino acids into proteins, and sequence the nucleotides on DNA strands.

Meyer explains:

To form a protein, amino acids must link together to form a chain. Yet amino acids form functioning proteins only when they adopt very specific sequential arrangements, rather like properly sequenced letters in an English sentence. Thus, amino acids alone do not make proteins, any more than letters alone make words, sentences, or poetry. In both cases, the sequencing of the constituent parts determines the function (or lack of function) of the whole.

…As it turns out, specific regions of the DNA molecule called coding regions have the same property of “sequence specificity” or “specified complexity” that characterizes written codes, linguistic texts, and protein molecules. Just as the letters in the alphabet of a written language may convey a particular message depending on their arrangement, so too do the sequences of nucleotide bases (the A’s, T’s, G’s, and C’s) inscribed along the spine of a DNA molecule convey a precise set of instructions for building proteins within the cell. The nucleotide bases in DNA function in precisely the same way as symbols in a machine code. In each case, the arrangement of the characters determines the function of the sequence as a whole…. In the case of DNA, the complex but precise sequencing of the four nucleotide bases (A, T, G, and C) stores and transmits the information necessary to build proteins.

…As Bernd–Olaf Kuppers recently stated, “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”

How do atheists account for this biological information?

Atheistic superstitions about the biological information

Le’s take a look at the atheist’s faith-based explanations of the origin of life: chance, law and self-organization.

For the first one, let’s calculate the odds of building a protein composed of a functional chain of 100 amino acids, by chance. (Think of a meaningful English sentence built with 100 scrabble letters, held together with glue)

1. Chance:

  • BONDING: You need 99 peptide bonds between the 100 amino acids. The odds of getting a peptide bond is 50%. The probability of building a chain of one hundred amino acids in which all linkages involve peptide bonds is roughly (1/2)^99 or 1 chance in 10^30.
  • CHIRALITY: You need 100 left-handed amino acids. The odds of getting a left-handed amino acid is 50%. The probability of attaining at random only L–amino acids in a hypothetical peptide chain one hundred amino acids long is (1/2)^100or again roughly 1 chance in 10^30.
  • SEQUENCE: You need to choose the correct amino acid for each of the 100 links. The odds of getting the right one are 1 in 20. Even if you allow for some variation, the odds of getting a functional sequence is (1/20)^100 or 1 in 10^65.

The final probability of getting a functional protein composed of 100 amino acids is 1 in 10^125. Even if you fill the universe with pre-biotic soup, and react amino acids at Planck time (very fast!) for 14 billion years, you are probably not going to get even 1 such protein. And you need at least 100 of them for minimal life functions, plus DNA and RNA.

Research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology, has shown that the number of functional amino acid sequences is tiny:

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly. He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 10^77.”

The problem of forming DNA by sequencing nucleotides faces similar difficulties. And remember, mutation and selection cannot explain the origin of the first sequence, because mutation and selection require replication, which does not exist until that first living cell is already in place.

2. Law:

The idea here is that components, such as nucleotides, might have special bonding affinities that might cause them to bond together spontaneously into functional sequences. Like if certain SCRABBLE tiles had an affinity for certain other tiles that caused them to bond together whenever they met.

Meyer writes:

Consider what would happen if the individual nucleotide “letters” in a DNA molecule did interact by chemical necessity with each other. Every time adenine (A) occurred in a growing genetic sequence, it would likely drag thymine (T) along with it. Every time cytosine (C) appeared, guanine (G) would follow. As a result, the DNA message text would be peppered with repeating sequences of A’s followed by T’s and C’s followed by G’s.

3. Self-organization:

The idea here is that some spontaneous order might arise due to some physical force, just like rocks sort themselves by size in a rock agitator because of gravity.

Meyer writes:

…just as magnetic letters can be combined and recombined in any way to form various sequences on a metal surface, so too can each of the four bases A, T, G, and C attach to any site on the DNA backbone with equal facility, making all sequences equally probable (or improbable). The same type of chemical bond occurs between the bases and the backbone regardless of which base attaches. All four bases are acceptable; none is preferred. In other words, differential bonding affinities do not account for the sequencing of the bases. Because these same facts hold for RNA molecules, researchers who speculate that life began in an “RNA world” have also failed to solve the sequencing problem…

Understanding what creates information

The bottom line is that in order for software code, or even English letters, to be functional, it needs to defy ordering mechanisms. Biological sequences are functional for the same reason that software code or English text is functional – because some intelligent agent chose an irregular sequence of characters in order to achieve a specific purpose. Look at the letters in this post – they are not ORDERED by physical laws. They are SELECTED by an intelligent agent.

Meyer writes:

To see the distinction between order and information, compare the sequence “ABABABABAB ABAB” to the sequence “Time and tide wait for no man.” The first sequence is repetitive and ordered, but not complex or informative.

What causes specified, complex sequences?

…the information contained in an English sentence or computer software does not derive from the chemistry of the ink or the physics of magnetism, but from a source extrinsic to physics and chemistry altogether. Indeed, in both cases, the message transcends the properties of the medium… Our experience with information–intensive systems (especially codes and languages) indicates that such systems always come from an intelligent source…

And this is what everybody means by “intelligent design”. This design inference came from the progress of science. The more we discovered about the cell, the more nature pointed towards a creative, designing intelligence. The only option left to atheists now is blind faith that the Flying Spaghetti Monster will swoop in and undo the progress of science over the last 100 years. Good luck with that, atheists!

Further study

One of my favorite resources on the origin of life is this interview from the University of California with former atheist and origin of life researcher Dean Kenyon. Kenyon, a professor of Biology at San Francisco State University, wrote the textbook on “chemical evolution”, which is the view that chemicals can arrange themselves in order to create the first living cell, without intervention.

This interview from the University of California with another origin of life researcher, Charles Thaxton, is also one of my favorites.

You’ll need Quicktime to see the videos, or buy the videos from ARN. (Kenyon, Thaxton) I have both of them – they rock!