Wintery Knight

…integrating Christian faith and knowledge in the public square

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.

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Study: the early Earth’s atmosphere contained oxygen

Here’s a paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”. This paper is significant because it undermines naturalistic scenarios for the origin of life.

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.

[...]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 DNA) 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 scenarios 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, oxygen levels, meteorite impacts, chirality, etc.

Most people who are talking about intelligent design at the origin of life talk about the information problem – how do you get the amino acids to form proteins and how do you get nucleotide bases to code for amino acids? But the starting point for solving the sequencing problem is the construction of the amino acids – there has to be a plausible naturalistic scenario to form them.

Filed under: News, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

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

Filed under: Polemics, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

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

Filed under: Polemics, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

New study: the early Earth’s atmosphere contained oxygen

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.

Filed under: News, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

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