Tag Archives: Evolution

Polemics

New software calculates the probability of generating functional proteins by chance

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Apologetics and the progress of science
Apologetics and the progress of science

Here’s an article sent to me by JoeCoder about a new computer program written by Kirk Durston.

About Kirk:

Kirk Durston is a scientist, a philosopher, and a clergyman with a Ph.D. in Biophysics, an M.A. in Philosophy, a B.Sc. in Mechanical Engineering, and a B.Sc. in Physics. His work involves a significant amount of time thinking, writing and speaking about the interaction of science, theology and philosophy within the context of authentic Christianity. He has been married for 34 years to Patti and they have six children and three grandchildren. He enjoys landscape photography, antiques of various types, wilderness canoeing and camping, fly fishing, amateur astronomy, reading, music, playing the saxophone (alto), and enjoying family and friends.

Kirk grew up on a cattle and grain farm in central Manitoba, Canada, where he spent countless hours wandering around on his own in the forest as a young boy, fascinated with the plants and animals that are native to that region of the province. Throughout his teen years he spent six days a week in the summer working as a farm hand with cattle and grain. He left his father’s farm at the age of 19 to go to university.

Canada? Can anything good come out of Canada? Oh well, at least he’s not from Scotland. Anyway, on to the research, that’s what we care about. Code!

Summary of the article:

  • Biological life requires proteins
  • Proteins are sequences of amino acids, chained together
  • the order of amino acids determines whether the sequence has biological function
  • sequences that have biological function are rare, compared to the total number of possible sequences
  • Durston wrote a program to calculate the number of the probability of getting a functional sequence by random chance
  • The probability for getting a functional protein by chance is incredibly low

With that said, we can understand what he wrote:

This program can compute an upper limit for the probability of obtaining a protein family from a wealth of actual data contained in the Pfam database. The first step computes the lower limit for the functional complexity or functional information required to code for a particular protein family, using a method published by Durston et al. This value for I(Ex) can then be plugged into an equation published by Hazen et al. in order to solve the probability M(Ex)/N of ‘finding’ a functional sequence in a single trial.

I downloaded 3,751 aligned sequences for the Ribosomal S7 domain, part of a universal protein essential for all life. When the data was run through the program, it revealed that the lower limit for the amount of functional information required to code for this domain is 332 Fits (Functional Bits). The extreme upper limit for the number of sequences that might be functional for this domain is around 10^92. In a single trial, the probability of obtaining a sequence that would be functional for the Ribosomal S7 domain is 1 chance in 10^100 … and this is only for a 148 amino acid structural domain, much smaller than an average protein.

For another example, I downloaded 4,986 aligned sequences for the ABC-3 family of proteins and ran it through the program. The results indicate that the probability of obtaining, in a single trial, a functional ABC-3 sequence is around 1 chance in 10^128. This method ignores pairwise and higher order relationships within the sequence that would vastly limit the number of functional sequences by many orders of magnitude, reducing the probability even further by many orders of magnitude – so this gives us a best-case estimate.

There are only about 10^80 particles in the entire physical universe – 10^85 at the most. These are long odds. But maybe if we expand the probabilistic resources by buying more slot machines, and we pull the slot machine lever at much faster rate… can we win the jackpot then?

Nope:

What are the implications of these results, obtained from actual data, for the fundamental prediction of neo-Darwinian theory mentioned above? If we assume 10^30 life forms with a fast replication rate of 30 minutes and a huge genome with a very high mutation rate over a period of 10 billion years, an extreme upper limit for the total number of mutations for all of life’s history would be around 10^43. Unfortunately, a protein domain such as Ribosomal S7 would require a minimum average of 10^100 trials, about 10^57 trials more than the entire theoretical history of life could provide – and this is only for one domain. Forget about ‘finding’ an average sized protein, not to mention thousands.

So even if you have lots of probabilistic resources, and lots of time, you’re still not going to get your protein.

Compare these numbers with the 1 in 10^77 number that I posted about yesterday from Doug Axe. There is just no way to account for proteins if there is no intelligent agent to place the amino acids in sequence. When it comes to writing code, writing blog posts, writing music, or placing Scrabble letters, you need an intelligence. Sequencing amino acids into proteins? You need an intelligence.

Polemics

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

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Apologetics and the progress of science
Apologetics and the progress of science

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.

Podcasts

Zack Kopplin debates Casey Luskin on science education

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Two Rams butting heads: may the best ram win!
Two Rams butting heads: may the best ram win!

The Michael Medved show is a national radio show broadcast out of Seattle, Washington. According to Talkers magazine, he has the fifth largest radio audience.

The MP3 file is available for download. (38 minutes)

The description is:

On this episode of ID the Future, the Medved Show hosts the CSC’s Casey Luskin and student Zack Kopplin, a leading activist in the effort to repeal the Louisiana Science Education Act. Luskin and Kopplin debate the implications of the Louisiana law for science education standards and whether or not the law promotes the teaching of creationism.

Topics:

  • Medved: Should teachers be forced to teach creationism in public schools?
  • Luskin: The Discovery Institute has never advocated that creationism be taught in public schools
  • Medved: Does the Louisiana law mandate that creationism be taught in public schools
  • Kopplin: Yes, the bill does because Bobby Jindal said that the bill teaches creationism
  • Luskin: (Reads the actual text of the law) the law EXPLICITLY STATES that teaching creationism is forbidden
  • Luskin: Governor Jindal is misinformed about the law, but if you look at the law it says NO CREATIONISM
  • Kopplin: I don’t care about what the law actually says, I’ll just repeat that Bobby Jindal thinks it’s creationism
  • Kopplin: Thirty years ago, there was an attempt to mandate creationism, therefore this law is doing the same thing
  • Medved: Are there any complaints that creationism is being taught in any schools after this law has been passed
  • Kopplin: No, I don’t know of any, but that’s not because there are none! Maybe there are some that I haven’t heard about yet
  • Medved: If you are taught something that you think is stupid, then is that automatically a violation of your rights?
  • Kopplin: Because you cannot allow the progress of science to call the religion of naturalism into question
  • Luskin: About that Jindal quote – he was talking about what he wanted to pass, not the law that actually passed
  • Luskin: (reads the text of the law again) The law explicitly says that teaching creationism in the classroom is prohibited
  • Luskin: Intelligent design is not creationism. Creationism starts with the Bible. Intelligent Design starts with science
  • Luskin: The law only supports teaching both sides of things that are already in the curriculum
  • Luskin: ID is not already in the curriculum, therefore, the law does not allow it to be discussed
  • Medved: Take Stephen C. Meyer’s book on the origin of life, could that be used in the classroom?
  • Kopplin: I am not very familiar with Meyer’s book, but if it is critical of Darwinism and naturalism, then it should not be taught. I don’t need to read it before I can censor it
  • Luskin: Meyer’s book advocates for ID, so it should not be taught in science classrooms
  • Luskin: non-ID science papers that are critical of Darwinism should be allowed in science classroom so students get both sides
  • Medved: Consider this brand new Oxford University Press book that is critical of Darwinian mechanisms, authored by Masatoshi Nei who is at Penn State University professor (written up on Evolution News)
  • Medved: Should this research critical of Darwinism be allowed in science classrooms?
  • Kopplin: I don’t know if this book should be allowed in science classrooms
  • Kopplin: I already know without reading anything though that there will never be evidence that supports intelligent design
  • Kopplin: There is no evidence against Darwinism and there is no controversy and there is no disagreement among scientists
  • Luskin: There are hundreds of papers in mainstream science peer-reviewed publications critical of Darwinism
  • Luskin: (lists a stack of papers critical of core tenets of Darwinian theory from respect science journals in the last few years)
  • Luskin: Masatoshi Nei recently posted a comment critical of the usefulness of the mutation-selection mechanism
  • Luskin: The real issue is whether students are allowed to hear mainstream scientific criticisms of Darwinism in the science classroom
  • Medved: Is it OK for a teacher to admit that on a specific issue in science, that there is no credible naturalistic explanation?
  • Kopplin: I am a history major, so I don’t want to comment on whether it is OK to admit that naturalism doesn’t explain everything
  • Luskin: A Harvard chemist says that the origin of life is an open issue in this peer-reviewed journal article
  • Luskin: Teachers should be allowed to say that there is no accepted naturalistic explanation for the origin of life
  • Luskin: teachers should NOT be teaching religion, or creationism, or even intelligent design in science classrooms
  • Luskin: but teachers should be allowed to say what the Harvard chemist said in that peer-reviewed article in the science classroom
  • Kopplin: there was a creationist woman who sat next to the Discovery Institute person when the law was being debated
  • Kopplin: so based on that there is a scary hidden creationist agenda behind the law which is not reflected in the actual text law
  • Luskin: Um, that woman has no connection to the Discovery Institute
  • Luskin: seating arrangement at the hearings were pre-determined, not selected by those in attendance
  • Luskin: what about people who are pushing Darwinism, who are anti-religious atheists and humanists? should they be disqualified?
  • Luskin: we should not discredit the arguments of either side based on speculations about their motives – what counts is the evidence
  • Kopplin: but I have a letter signed by lots of Nobel-prize winning scientists that opposes the Louisiana science education law
  • Luskin: but that letter never actually quotes from the law, it is critiquing views that have nothing to do with the actual law
  • Medved: Summarize your views
  • Kopplin: Criticism of Darwinism and naturalism using mainstream scientific evidence SHOULD NOT be allowed in the science classroom
  • Luskin: Criticism of Darwinism and naturalism using mainstream scientific evidence SHOULD be allowed in the science classroom

And there is a period of questions from the callers.

This episode features a debate, so it is not to be missed. it is always a good idea to hear both sides. Unfortunately, ID people are the only ones who think that both sides should be heard.

I subscribe to the ID the Future podcast, and I really recommend that you do as well!