Tag Archives: Noodly Appendage

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

Do the Miller-Urey experiments simulate the early Earth?
Do the Miller-Urey experiments simulate the early Earth?

The origin of life

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

  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 naturalist all the building blocks he needs. This is because step 2 is impossible. There is no way, on naturalism, 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 a topic for a separate post.

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.

Positive arguments for Christian theism

 

How likely is it for blind forces to sequence a functional protein by chance?

How likely is it that you could swish together amino acids randomly and come up with a sequence that would fold up into a functional protein?

Evolution News reports on research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology.

Excerpt:

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.10 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.”11 The extreme unlikelihood of finding functional proteins has important implications for intelligent design.

Just so you know, those footnotes say this:

[10.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004); Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000).

[11.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004).

And remember, you need a lot more than just 1 protein in order to create even the simplest living system. Can you generate that many proteins in the short time between when the Earth cools and the first living cells appear? Even if we spot the naturalist a prebiotic soup as big as the universe, and try to make sequences as fast as possible, it’s unlikely to generate even one protein in the time before first life appears.

Here’s Doug Axe to explain his research:

If you are building a protein for the FIRST TIME, you have to get it right all at once – not by building up to it gradually using supposed Darwinian mechanisms. That’s because there is no replication before you have the first replicator. The first replicator cannot rely on explanations that require replication to already be in place.

Doug Axe explains the chances of getting a functional protein by chance

I’ve talked about Doug Axe before when I described how to calculate the odds of getting functional proteins by chance.

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)

Sub-problems:

  • 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)^100 or 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.

But you can’t show that to your friends, you need to send them a video. And I have a video!

A video of Doug Axe explaining the calculation

Here’s a clip from Illustra Media’s new ID DVD “Darwin’s Dilemma”, which features Doug Axe and Stephen Meyer (both with Ph.Ds from Cambridge University).

I hope you all read Brian Auten’s review of Darwin’s Dilemma! It was awesome.

Related DVDs

Illustra also made two other great DVDs on intelligent design. The first two DVDs “Unlocking the Mystery of Life” and “The Privileged Planet” are must-buys, but you can watch them on youtube if you want, for free.

Here are the 2 playlists:

I also recommend Coldwater Media’s “Icons of Evolution”. All three of these are on sale from Amazon.com.

Related posts

Doug Axe explains the chances of getting a functional protein by chance

I’ve talked about Doug Axe before when I described how to calculate the odds of getting functional proteins by chance.

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)

Sub-problems:

  • 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)^100 or 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.

But you can’t show that to your friends, you need to send them a video. And I have a video!

A video of Doug Axe explaining the calculation

Here’s a clip from Illustra Media’s new ID DVD “Darwin’s Dilemma”, which features Doug Axe and Stephen Meyer (both with Ph.Ds from Cambridge University).

I hope you all read Brian Auten’s review of Darwin’s Dilemma! It was awesome.

Related DVDs

Illustra also made two other great DVDs on intelligent design. The first two DVDs “Unlocking the Mystery of Life” and “The Privileged Planet” are must-buys, but you can watch them on youtube if you want, for free.

Here are the 2 playlists:

I also recommend Coldwater Media’s “Icons of Evolution”. All three of these are on sale from Amazon.com.

Related posts

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

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!