Tag Archives: Building

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

Why would God want us to praise him?

From Amy K. Hall, staff apologist at Stand to Reason. (H/T The Poached Egg)

Excerpt:

I was recently asked why God would want us to praise and worship Him. This is a question I hear every so often since we immediately assume that a person who demands praise is a pompous big-head. I think there are many Christians out there who secretly wonder about this—afraid to ask the question (lest they be thought unspiritual), but bothered all the same.

God is completely self-sufficient and doesn’t need our praise and worship. However, He does deserve it. Would you agree that it is right and good to praise someone who is worthy of praise? We instinctively know this and praise people for all sorts of achievements. We praise the people we love and admire, and it’s not right or good for us to withhold praise from them.

We all understand the concept of praise being due certain people. Imagine that you crafted an incredibly beautiful sculpture and won a prestigious award for your creation; but when the time came for the award ceremony, they gave the prize for your sculpture to the wrong artist! That would not be just, right, or good. In the same way, God—as the only being perfect in goodness, justice, love, etc.—is worthy of our praise. We do, in fact, owe Him that praise. He wants us to praise Him because it is right and good for us to do so. Since God wants us to do right and good things, of course he wants us to praise and worship Him.

Beyond the praise being right and good (and because of its being right and good), worshiping God also brings us joy and enhances our relationship with Him. We see this in human relationships as well—think of a man with his wife. Doesn’t it bring him great joy to praise her?

I think it it’s interesting to note that very often, non-theists try to explain things like the creation of the universe and the fine-tuning of the universe and the origin of life as being the result of blind forces. That is the opposite of praise – that is speculating about nature to avoid giving credit to nature’s Creator and Designer. They are trying to escape the obligation to worship by attributing the great miracles of God to no one, so they can be accountable to no one. This is not the kind of thought life that God looks kindly on.

One important result of studying the world, including science, is to be able to understand what God has done in the world and to give him appropriate recognition for it. It is part of being in a relationship with him that we know him and respond appropriately to his real character. The refusal to acknowledge God is one of the symptoms of rebellion against him.

Matthew 10:32-33:

 32 “Whoever acknowledges me before others, I will also acknowledge before my Father in heaven.

33 But whoever disowns me before others, I will disown before my Father in heaven.

And this also appears in Luke 12:8-10:

8 “And I tell you, everyone who acknowledges me before men, the Son of Man also will acknowledge before the angels of God,

9 but the one who denies me before men will be denied before the angels of God.

10 And everyone who speaks a word against the Son of Man will be forgiven, but the one who blasphemes against the Holy Spirit will not be forgiven.

This passage is an early passage from Q, because it’s shared by Matthew and Luke, and Q is a source for those two early gospels. To get on the right side of this verse, it’s important to study what God has done, so you can give him the praise that he has earned. He wants to be acknowledged, and we want to hold up our end of the relationship and give him that acknowledgement. He did the deeds, and that means he should get the recognition for it.

One more thing I want to say about this. I see a lot of people singing songs about God in church, expressing praise for things they have no reason to believe that God has done. I think a good way to have authentic praise for God is to tone down the singing in groups and the emotional highs and the pretty buildings for a while, and focus on apologetics. Focus on learning the real stuff that God has actually done that we can know about – by studying science and history. In fact, it really scares me when I see young people singing and raising their hands and closing their eyes at church when I know good and well they have no intellectual grounding for these activities – it makes me feel like I am in some cult or something, surrounded by self-serving, fun-seeking weirdos.

You know that brings up an interesting question. What do you suppose would happen if I gathered together all the pastors and singing church people into a room and told them that we were going to do a scientific study of what God has done in nature, and a historical study of what God has done in history? My guess is that they would attack me, drive me out of the church, and go back to singing songs in groups with big musical bands and colorful lights in the ceiling. I think we need to guard against making Christianity about feelings and experiences and group gatherings, and make it more about knowledge. What has God really done that we can know about?

Let’s lay down a base of knowledge about God from nature and history, and then once we know he is real and he is good, we can talk about theology, and praising him for all of that. We don’t want what we do in church to be in anyway comparable to what non-Christians do in night clubs and concerts – gathering in groups and dancing around ecstatically. Blech! Christianity is about truth, not feelings.

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.

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!