Tag Archives: Dawkins

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

Coward A.C. Grayling and chicken Dawkins flee debate with William Lane Craig

Sing with me:

Brave Sir Grayling ran away
Bravely, ran away…away…
When danger reared its ugly head
He bravely turned his tail and fled
Yes, brave Sir Grayling turned about
And gallantly he chickened out
Bravely taking to his feet
He beat a very brave retreat
Bravest of the brave, Sir Grayling

He is packing it in and packing it up
And sneaking away and buggering off
And chickening out and pissing off home,
Yes, bravely he is throwing in the sponge.

From BeThinking.org’s web site.

Excerpt:

For years, ‘New Atheist’ Professors Anthony Grayling and Richard Dawkins have made money and gained publicity out of God.  But now, the courage of their convictions seems to be running dry: they have both refused to debate one of the world’s leading defenders of the Christian Faith, Professor William Lane Craig.

While Professor Dawkins has set himself up as the ‘scourge’ of the Church, Professor Grayling has offered his latest attack on Christianity by publishing The Good Book – a secular bible in the year the Church celebrates the 400th anniversary of the translation of the King James Bible.

While Dawkins and Grayling have refused to debate the existence of God, Grayling has also refused to debate the foundations of the morality on which his ‘Good Book’ rests. These point-blank refusals to engage in public discussions with Professor Craig will undermine their credibility, not only among Christians but also amongst fellow academics.

Professor Craig, Research Professor of Philosophy at Talbot School of Theology, California, is arguably the world’s foremost defender of historic Christianity. He has debated with many top academics and leading atheists across the world, including Peter Atkins, Daniel Dennett, Anthony Flew, Christopher Hitchens, Lewis Wolpert and, most recently, Sam Harris.

Craig visited the UK in 2007 and received national media coverage for his debate at Westminster Central Hall with Professor Lewis Wolpert, chaired by Radio 4’s Today presenter, John Humphrys. This debate has now been seen by thousands of people on YouTube. Professor Craig, who has two Ph.Ds, has written over thirty books and published some 200 academic papers. He is returning to the UK from 17-26 October in a tour sponsored by the Universities and Colleges Christian Fellowship, Damaris Trust and Premier Christian Radio.

Having been invited to debate Craig, Professor Grayling replied:

I am not interested in debating Professor Craig, though if he would like to co-opt me for the publicity for his tour – I would be happy to debate him on the question of the existence of fairies and water-nymphs. But as for the very uninteresting matter of whether there is just one god or goddess and that it can be debated despite the claim that it is transcendently ineffable and unknowablethat is an empty prospect, hence my declining the invitation.”

Justin Brierley, who presents Premier Radio’s highly-rated discussion programme, Unbelievable?, comments:

“It looks insulting and worryingly narrow minded when an invitation to defend such views against a top-flight Christian academic such as Dr. Craig is dismissed in these terms. Grayling is seen as a key proponent of rationalism and atheism in the UK. It will therefore come as a surprise to many that he is so unwilling to defend the rational grounds for atheism against a major opponent.”

Brian Auten of Apologetics 315 tweeted this, earlier:

If you would like the see how well atheists do in debates with Craig, you can watch this:

William Lane Craig vs. Christopher Hitchens:

No wonder Grayling and Dawkins are soiling their knickers at the thought of facing him. It’s easy to impress your students when you are grading their papers AFTER they’ve paid their tuition. But a formal debate in a neutral venue would not be safe.

Previous story on Dawkins’ refusal to debate is here.

Craig’s UK tour schedule is here.

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

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!