Tag Archives: Computer Science

New software calculates the probability of generating functional proteins by chance

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.

Michael Ruse debates Stephen C. Meyer on intelligent design and evolution on NPR

Here’s a debate between:

  • Stephen C. Meyer, author of Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
  • Michael Ruse, Director of the History and Philosophy of Science Program at Florida State University

The MP3 file is here. (28 minutes)

The following summary is rated S for Slightly Snarky. Reader discretion is advised.

Topics:

  • Moderator: (to Meyer) define creationism, evolution, and intelligent design
  • Meyer: creationism is based on an interpretation of the Bible
  • Meyer: evolution is an unguided process of mutation and selection that produces organisms
  • Meyer: intelligent design is the idea that the best explanation for certain features of life
  • Moderator: (to Ruse) Where do you disagree?
  • Ruse: Intelligent design is similar to creationism, but I won’t say how exactly
  • Meyer: ID is a good explanation for the sudden origin of animal body plans in the Cambrian era
  • Moderator: (to Meyer) Is the designer God? Is the designer the Christian God?
  • Meyer: No, ID theory is an inference that is rooted in scientific evidence, not in a religious text
  • Meyer: ID can be inferred from the origin of biological information and from molecular machines
  • Moderator: (to Ruse) Where do you disagree?
  • Ruse: Meyer is disingenuous because ID requires the designer to be God
  • Meyer: The biological evidence for intelligent design by itself does not implicate God
  • Meyer: The fine-tuning of the cosmos is intelligent design in physics, and that *would* require God
  • Moderator: (to Meyer) Explain what the Cambrian explosion is
  • Meyer: sudden origin of 36 body plans in 10 million years 530 million years ago
  • Moderator: So you think that 36 body plans in 10 million years is too sudden for Darwinian mechanisms to produce?
  • Meyer: Yes, for two reasons. One, there are no precursors prior to the start of the explosion in complexity
  • Meyer: And two, the complexity of animal life includes code, circuitry, hierarchies – best explained by a designer
  • Moderator: (to Ruse) Is it a problem for you?
  • Ruse: There is no peer-reviewed paper that denies that the Ediacaran fauna are precursors to the Cambrian animals
  • Ruse: There is no peer-reviewed paper that denies that microfossils are precursors to the Cambrian animals
  • Ruse: There is no peer-reviewed paper that denies that animal complexity goes from simple to complex in the fossil record
  • Ruse: There is no peer-reviewed paper that shows that the Cambrian explosion took place over a few million years
  • Ruse: There is no peer-reviewed paper that shows that there were complex organ types at the start of the Cambrian explosion
  • Ruse: There is no peer-reviewed paper that denies that we already have a materialist explanation for the Cambrian explosion
  • Ruse: everything is solved! nothing to see here! (folds arms and beams) I trust that my unsupported assertions have relieved your doubts, yes?
  • Moderator: Is intelligent design undermined by more recent science?
  • Meyer: no, there is an absence of precursor fossils in the period before the Cambrian explosion
  • Meyer: there are other things that make the problem even worse for naturalism, like information from epigenetics
  • Moderator: (to Ruse) Answer that
  • Ruse: He is just pulling out passages out of context because he is a creationist!
  • Moderator: The leftist New Yorker reviewer Gareth Cook says that the Cambrian explosion took tens of millions of years
  • Meyer: Actually, the peer-reviewed science is clear that the standard date is at most 10 million nears
  • Moderator: (to Ruse) Deny the mainstream date
  • Ruse: Well, Prothero says no! Ho ho ho! (folds arms) He just says it. No it’s not published in peer-reviewed research
  • Ruse: We know so much more than Darwin did, how could the progress of science disprove my materialist pre-supposition? It’s unpossible!
  • Moderator: (to Meyer) Isn’t ID pseudo-science?
  • Meyer: If we limit ourselves to materialist explanations only, then we cannot infer intelligence when we see artifacts like the Rosetta Stone
  • Meyer: wind and erosion is not an adequate explanation for certain systems – systems that are rich in information
  • Meyer: the best explanation is the explanation that relies on known causes – we know that intelligence produces information
  • Moderator: (to Meyer) so the intelligence is the best explanation of systems that have information?
  • Meyer: yes, think about software code – the best explanation of new computer instructions is an intelligence
  • Meyer: we have uniform and repeated experience of intelligence bringing new information into being, and new animals need new information
  • Moderator: (to Ruse) must science only work with natural explanations?
  • Ruse: intelligent design is religion! Ho ho ho ho! (folds arms)
  • Ruse: there is no a priori way of ruling out supernatural causes in order to explain nature
  • Ruse: We don’t need to introduce supernatural causes to explain information in living systems or in software code
  • Ruse: Steve is asking me to explain the Cambrian explosion, but why does he want me to explain that?
  • Ruse: How did anything start to fly? How did whales come? There, those questions explain the Cambrian explosion naturalistically
  • Ruse: Steve’s answer to explain new information is to bring in miracles, like when he said that new computer code requires God
  • Ruse: inferring intelligence as an explanation for information like the computer code is religion! God! Creationism! Prayer in schools!
  • Ruse: we have to keep looking for naturalistic explanations for the Big Bang, the DNA, the fine-tuning, the Cambrian fossils, etc.
  • Ruse: we are never justified in inferring an intelligence to explain information, because that would deny my religion of materialism
  • Moderator: (to Ruse) what are the requirements for a theory to be scientific?
  • Ruse: any explanation has to be naturalistic, because I am an atheist and that’s my religion, and we can’t go against my religion
  • Ruse: it’s “really stupid” to infer God as the explanation of the creation of the entire physical universe or the cosmic fine-tuning
  • Moderator: (to Meyer) why is intelligent design so popular when we have court cases saying it is not science?
  • Meyer: the Discovery Institute does not have an agenda to teach intelligent design in public schools
  • Meyer: intelligent design is about inferring intelligence as a causal explanation for information in living systems, and elsewhere
  • Moderator: (to Ruse) are evolutionists unwilling to entertain the possibility of intelligence being the best explanation?
  • Ruse: scientists have to make sure that that all their explanations don’t go outside of the materialist reservation
  • Ruse: intelligent design is evangelical Christianity dressed up to look like science, the Dover judge said so
  • Ruse: Meyer is disingenuous! Ho ho ho ho ho! (folds arms contentedly)
  • Meyer: first, judges don’t decide science, evidence decides science
  • Meyer: the Dover people made a mistake by trying to go to the courts to get things into the schools
  • Meyer: intelligent design is about research, writing books and papers based on what we learn from science
  • Moderator: (to Ruse) is intelligent design dangerous?
  • Ruse: yes, intelligent design is about politics, it’s not about cosmic fine-tuning, origin of life, molecular machines or Cambrian explosion
  • Ruse: intelligent design is about abstinence, prayer in schools, burdening women with unwanted babies and male-female marriage
  • Ruse: my reason for opposing ID is the socially conservative agenda which emerges from protein folding probability calculations
  • Ruse: I don’t want to be drafted to fight in Vietnam, I don’t want them to take away my drugs, etc. so that’s why I believe Darwinism
  • Moderator: (to Meyer) why do you want to take abortion away, you meany?
  • Meyer: actually, intelligent design is about science, and in any case National Review gave my book a bad review
  • Moderator: (to Ruse) are science and religion in conflict?
  • Ruse: well religion can just abstain from making any claims about the physical world, and just stick to subjective nonsense – that’s fair
  • Moderator: (to Meyer) isn’t all opposition to evolution rooted in fundamentalist religion?
  • Meyer: you can believe in Darwinism and be a theist, but the real reason for doubting Darwinism is the scientific evidence, not religion

Tell me how you think Dr. Meyer did in the comments.

Stephen C. Meyer debates Peter D. Ward on intelligent design and evolution

The speakers

Stephen C. Meyer is director of the Discovery Institute’s Center for Science and Culture (CSC) and a founder both of the intelligent design movement and of the CSC, intelligent design’s primary intellectual and scientific headquarters. Dr. Meyer is a Cambridge University-trained philosopher of science, the author of peer-reviewed publications in technical, scientific, philosophical and other books and journals. His signal contribution to ID theory is given most fully in Signature in the Cell: DNA and the Evidence for Intelligent Design, published by HarperOne in June 2009.

Graduating from Whitworth College in Spokane, Washington, in 1981 with a degree in physics and earth science, he later became a geophysicist with Atlantic Richfield Company (ARCO) in Dallas, Texas. From 1981 to 1985, he worked for ARCO in digital signal processing and seismic survey interpretation. As a Rotary International Scholar, he received his training in the history and philosophy of science at Cambridge University, earning a PhD in 1991. His thesis offered a methodological interpretation of origin-of-life research.

Peter D. Ward, Ph.D., is a paleontologist and professor in the Departments of Geology and Biology at the University of Washington in Seattle. He also serves as an adjunct professor of zoology and astronomy. His research specialties include the Cretaceous–Tertiary extinction event and mass extinctions generally. His books include the best-selling “Rare Earth: Why Complex Life Is Uncommon in the Universe” (co-author Donald Brownlee, 2000), “Under a Green Sky: Global Warming, the Mass Extinctions of the Past, and What They Can Tell Us About Our Future” (2007), and “The Medea Hypothesis: Is Life on Earth Ultimately Self-Destructive?” (2009).

The debate

Here’s the video of the debate:

The debate itself starts at around 8:19, after all the moderators have spoken.

The debate is focused on disagreements about scientific evidence.

Even though Peter Ward is an atheist, he has co-written a fabulous book that I own and have read called “Rare Earth: Why Complex Life is Uncommon in the Universe“. I really recommend getting this book, as it is a great book by two non-theists on the habitability argument. It’s sort of a secular precursor to Jay Richards’ and Guillermo Gonzalez’s “The Privileged Planet: How Our Place in the Cosmos is Designed for Discovery“. The habitability argument is a really neglected argument, but it’s a good one.

Michael Ruse debates Stephen C. Meyer on intelligent design and evolution on NPR

Details: (from NPR web site)

About one third of Americans believe in intelligent design, according to a recent Gallup poll. That’s the idea that humans evolved over time from lesser life forms – with the process guided by God. It’s added a new dimension to the old debate over where humans come from and raised serious concern in the scientific world about mixing faith with science.

  • Stephen C. Meyer, author of Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
  • Michael Ruse, Director of the History and Philosophy of Science Program at Florida State University

The MP3 file is here. (28 minutes)

The following summary is rated S for Slightly Snarky. Reader discretion is advised.

Topics:

  • Moderator: (to Meyer) define creationism, evolution, and intelligent design
  • Meyer: creationism is based on an interpretation of the Bible
  • Meyer: evolution is an unguided process of mutation and selection that produces organisms
  • Meyer: intelligent design is the idea that the best explanation for certain features of life
  • Moderator: (to Ruse) Where do you disagree?
  • Ruse: Intelligent design is similar to creationism, but I won’t say how exactly
  • Meyer: ID is a good explanation for the sudden origin of animal body plans in the Cambrian era
  • Moderator: (to Meyer) Is the designer God? Is the designer the Christian God?
  • Meyer: No, ID theory is an inference that is rooted in scientific evidence, not in a religious text
  • Meyer: ID can be inferred from the origin of biological information and from molecular machines
  • Moderator: (to Ruse) Where do you disagree?
  • Ruse: Meyer is disingenuous because ID requires the designer to be God
  • Meyer: The biological evidence for intelligent design by itself does not implicate God
  • Meyer: The fine-tuning of the cosmos is intelligent design in physics, and that *would* require God
  • Moderator: (to Meyer) Explain what the Cambrian explosion is
  • Meyer: sudden origin of 36 body plans in 10 million years 530 million years ago
  • Moderator: So you think that 36 body plans in 10 million years is too sudden for Darwinian mechanisms to produce?
  • Meyer: Yes, for two reasons. One, there are no precursors prior to the start of the explosion in complexity
  • Meyer: And two, the complexity of animal life includes code, circuitry, hierarchies – best explained by a designer
  • Moderator: (to Ruse) Is it a problem for you?
  • Ruse: There is no peer-reviewed paper that denies that the Ediacaran fauna are precursors to the Cambrian animals
  • Ruse: There is no peer-reviewed paper that denies that microfossils are precursors to the Cambrian animals
  • Ruse: There is no peer-reviewed paper that denies that animal complexity goes from simple to complex in the fossil record
  • Ruse: There is no peer-reviewed paper that shows that the Cambrian explosion took place over a few million years
  • Ruse: There is no peer-reviewed paper that shows that there were complex organ types at the start of the Cambrian explosion
  • Ruse: There is no peer-reviewed paper that denies that we already have a materialist explanation for the Cambrian explosion
  • Ruse: everything is solved! nothing to see here! (folds arms and beams) I trust that my unsupported assertions have relieved your doubts, yes?
  • Moderator: Is intelligent design undermined by more recent science?
  • Meyer: no, there is an absence of precursor fossils in the period before the Cambrian explosion
  • Meyer: there are other things that make the problem even worse for naturalism, like information from epigenetics
  • Moderator: (to Ruse) Answer that
  • Ruse: He is just pulling out passages out of context because he is a creationist!
  • Moderator: The leftist New Yorker reviewer Gareth Cook says that the Cambrian explosion took tens of millions of years
  • Meyer: Actually, the peer-reviewed science is clear that the standard date is at most 10 million nears
  • Moderator: (to Ruse) Deny the mainstream date
  • Ruse: Well, Prothero says no! Ho ho ho! (folds arms) He just says it. No it’s not published in peer-reviewed research
  • Ruse: We know so much more than Darwin did, how could the progress of science disprove my materialist pre-supposition? It’s unpossible!
  • Moderator: (to Meyer) Isn’t ID pseudo-science?
  • Meyer: If we limit ourselves to materialist explanations only, then we cannot infer intelligence when we see artifacts like the Rosetta Stone
  • Meyer: wind and erosion is not an adequate explanation for certain systems – systems that are rich in information
  • Meyer: the best explanation is the explanation that relies on known causes – we know that intelligence produces information
  • Moderator: (to Meyer) so the intelligence is the best explanation of systems that have information?
  • Meyer: yes, think about software code – the best explanation of new computer instructions is an intelligence
  • Meyer: we have uniform and repeated experience of intelligence bringing new information into being, and new animals need new information
  • Moderator: (to Ruse) must science only work with natural explanations?
  • Ruse: intelligent design is religion! Ho ho ho ho! (folds arms)
  • Ruse: there is no a priori way of ruling out supernatural causes in order to explain nature
  • Ruse: We don’t need to introduce supernatural causes to explain information in living systems or in software code
  • Ruse: Steve is asking me to explain the Cambrian explosion, but why does he want me to explain that?
  • Ruse: How did anything start to fly? How did whales come? There, those questions explain the Cambrian explosion naturalistically
  • Ruse: Steve’s answer to explain new information is to bring in miracles, like when he said that new computer code requires God
  • Ruse: inferring intelligence as an explanation for information like the computer code is religion! God! Creationism! Prayer in schools!
  • Ruse: we have to keep looking for naturalistic explanations for the Big Bang, the DNA, the fine-tuning, the Cambrian fossils, etc.
  • Ruse: we are never justified in inferring an intelligence to explain information, because that would deny my religion of materialism
  • Moderator: (to Ruse) what are the requirements for a theory to be scientific?
  • Ruse: any explanation has to be naturalistic, because I am an atheist and that’s my religion, and we can’t go against my religion
  • Ruse: it’s “really stupid” to infer God as the explanation of the creation of the entire physical universe or the cosmic fine-tuning
  • Moderator: (to Meyer) why is intelligent design so popular when we have court cases saying it is not science?
  • Meyer: the Discovery Institute does not have an agenda to teach intelligent design in public schools
  • Meyer: intelligent design is about inferring intelligence as a causal explanation for information in living systems, and elsewhere
  • Moderator: (to Ruse) are evolutionists unwilling to entertain the possibility of intelligence being the best explanation?
  • Ruse: scientists have to make sure that that all their explanations don’t go outside of the materialist reservation
  • Ruse: intelligent design is evangelical Christianity dressed up to look like science, the Dover judge said so
  • Ruse: Meyer is disingenuous! Ho ho ho ho ho! (folds arms contentedly)
  • Meyer: first, judges don’t decide science, evidence decides science
  • Meyer: the Dover people made a mistake by trying to go to the courts to get things into the schools
  • Meyer: intelligent design is about research, writing books and papers based on what we learn from science
  • Moderator: (to Ruse) is intelligent design dangerous?
  • Ruse: yes, intelligent design is about politics, it’s not about cosmic fine-tuning, origin of life, molecular machines or Cambrian explosion
  • Ruse: intelligent design is about abstinence, prayer in schools, burdening women with unwanted babies and male-female marriage
  • Ruse: my reason for opposing ID is the socially conservative agenda which emerges from protein folding probability calculations
  • Ruse: I don’t want to be drafted to fight in Vietnam, I don’t want them to take away my drugs, etc. so that’s why I believe Darwinism
  • Moderator: (to Meyer) why do you want to take abortion away, you meany?
  • Meyer: actually, intelligent design is about science, and in any case National Review gave my book a bad review
  • Moderator: (to Ruse) are science and religion in conflict?
  • Ruse: well religion can just abstain from making any claims about the physical world, and just stick to subjective nonsense – that’s fair
  • Moderator: (to Meyer) isn’t all opposition to evolution rooted in fundamentalist religion?
  • Meyer: you can believe in Darwinism and be a theist, but the real reason for doubting Darwinism is the scientific evidence, not religion

Tell me how you think Dr. Meyer did in the comments. I think that Ruse is a Darwinist because he views it as a way to push people away from the conservative morality and politics. But he’s a nice guy, and I appreciate him debating the issue. Things are tough right now for his side.

Stephen C. Meyer debates Peter D. Ward on intelligent design and evolution

The speakers

Stephen C. Meyer is director of the Discovery Institute’s Center for Science and Culture (CSC) and a founder both of the intelligent design movement and of the CSC, intelligent design’s primary intellectual and scientific headquarters. Dr. Meyer is a Cambridge University-trained philosopher of science, the author of peer-reviewed publications in technical, scientific, philosophical and other books and journals. His signal contribution to ID theory is given most fully in Signature in the Cell: DNA and the Evidence for Intelligent Design, published by HarperOne in June 2009.

Graduating from Whitworth College in Spokane, Washington, in 1981 with a degree in physics and earth science, he later became a geophysicist with Atlantic Richfield Company (ARCO) in Dallas, Texas. From 1981 to 1985, he worked for ARCO in digital signal processing and seismic survey interpretation. As a Rotary International Scholar, he received his training in the history and philosophy of science at Cambridge University, earning a PhD in 1991. His thesis offered a methodological interpretation of origin-of-life research.

Peter D. Ward, Ph.D., is a paleontologist and professor in the Departments of Geology and Biology at the University of Washington in Seattle. He also serves as an adjunct professor of zoology and astronomy. His research specialties include the Cretaceous–Tertiary extinction event and mass extinctions generally. His books include the best-selling “Rare Earth: Why Complex Life Is Uncommon in the Universe” (co-author Donald Brownlee, 2000), “Under a Green Sky: Global Warming, the Mass Extinctions of the Past, and What They Can Tell Us About Our Future” (2007), and “The Medea Hypothesis: Is Life on Earth Ultimately Self-Destructive?” (2009).

The debate

Here’s the video of the debate:

The debate itself starts at around 8:19, after all the moderators have spoken.

The debate is focused on disagreements about scientific evidence.

Even though Peter Ward is an atheist, he has co-written a fabulous book that I own and have read called “Rare Earth: Why Complex Life is Uncommon in the Universe“. I really recommend getting this book, as it is a great book by two non-theists on the habitability argument. It’s sort of a secular precursor to Jay Richards’ and Guillermo Gonzalez’s “The Privileged Planet: How Our Place in the Cosmos is Designed for Discovery“. The habitability argument is a really neglected argument, but it’s a good one.