Tag Archives: Origin of Life

Yale University computer science professor takes a look at protein formation probabilities

How did life begin?
How did life begin?

When I was in graduate school, we studied a book called “Mirror Worlds”, authored by famous computer science professor David Gelernter at Yale University. This week, I noticed that Dr. Gelernter had written an article in the prestigious Claremont Review of Books. In his article, he applies his knowledge of computer science to the problem of the origin of life.

Evolution, if it is going to work at all, has to explain the problem of how the basic building blocks of life – proteins – can emerge from non-living matter. It turns out that the problem of the origin of life is essentially a problem of information – of code. If the components of proteins are ordered properly, then the sequence folds up into a protein that has biological function. If the sequence is not good, then just like computer code, it won’t run.

Here’s Dr. Gelernter to explain:

How to make proteins is our first question. Proteins are chains: linear sequences of atom-groups, each bonded to the next. A protein molecule is based on a chain of amino acids; 150 elements is a “modest-sized” chain; the average is 250. Each link is chosen, ordinarily, from one of 20 amino acids. A chain of amino acids is a polypeptide—“peptide” being the type of chemical bond that joins one amino acid to the next. But this chain is only the starting point: chemical forces among the links make parts of the chain twist themselves into helices; others straighten out, and then, sometimes, jackknife repeatedly, like a carpenter’s rule, into flat sheets. Then the whole assemblage folds itself up like a complex sheet of origami paper. And the actual 3-D shape of the resulting molecule is (as I have said) important.

Imagine a 150-element protein as a chain of 150 beads, each bead chosen from 20 varieties. But: only certain chains will work. Only certain bead combinations will form themselves into stable, useful, well-shaped proteins.

So how hard is it to build a useful, well-shaped protein? Can you throw a bunch of amino acids together and assume that you will get something good? Or must you choose each element of the chain with painstaking care? It happens to be very hard to choose the right beads.

Gelernter decides to spot the Darwinist a random sequence of 150 elements. Now the task the Darwinist is to use random mutation to arrive at a sequence of 150 links that has biological function.

[W]hat are the chances that a random 150-link sequence will create such a protein? Nonsense sequences are essentially random. Mutations are random. Make random changes to a random sequence and you get another random sequence. So, close your eyes, make 150 random choices from your 20 bead boxes and string up your beads in the order in which you chose them. What are the odds that you will come up with a useful new protein?

[…]The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20150. In other words, many. 20150 roughly equals 10195, and there are only 1080 atoms in the universe.

What proportion of these many polypeptides are useful proteins? Douglas Axe did a series of experiments to estimate how many 150-long chains are capable of stable folds—of reaching the final step in the protein-creation process (the folding) and of holding their shapes long enough to be useful. (Axe is a distinguished biologist with five-star breeding: he was a graduate student at Caltech, then joined the Centre for Protein Engineering at Cambridge. The biologists whose work Meyer discusses are mainly first-rate Establishment scientists.) He estimated that, of all 150-link amino acid sequences, 1 in 1074 will be capable of folding into a stable protein. To say that your chances are 1 in 1074 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller. Axe puts them at 1 in 1077.

In other words: immense is so big, and tiny is so small, that neo-Darwinian evolution is—so far—a dead loss. Try to mutate your way from 150 links of gibberish to a working, useful protein and you are guaranteed to fail. Try it with ten mutations, a thousand, a million—you fail. The odds bury you. It can’t be done.

Keep in mind that you need many, many proteins in order to have even a simple living cell. (And that’s not even considering the problem of organizing the proteins into a system).

So, if you’re a naturalist, then your only resources to explain the origin of life are chance and mutation. As Dr. Gelernter shows, naturalistic explanations won’t work to solve even part of the problem. Not even with a long period of time.  Not even if you use the entire universe as one big primordial soup, and keep trying sequences for the history of the universe. It just isn’t possible to arrive at sequences that have biological function in the time available, using the resources available. The only viable explanation is that there is a computer scientist who wrote the code without using trial and error. Something that ordinary software engineers like myself and Dr. Gelernter do all the time. We know what kind of cause is adequate to explain functioning code.

The importance of having a narrative when confronting the assumption of naturalism

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

How do you present theism as a rational belief to a person who thinks that the progress of science has removed the need for God?

Canadian science writer Denyse O’Leary writes about the history of cosmology at Evolution News.

Excerpt:

What help has materialism been in understanding the universe’s beginnings?

Many in cosmology have never made any secret of their dislike of the Big Bang, the generally accepted start to our universe first suggested by Belgian priest Georges Lemaître (1894-1966).

On the face of it, that is odd. The theory accounts well enough for the evidence. Nothing ever completely accounts for all the evidence, of course, because evidence is always changing a bit. But the Big Bang has enabled accurate prediction.

In which case, its hostile reception might surprise you. British astronomer Fred Hoyle (1915-2001) gave the theory its name in one of his papers — as a joke. Another noted astronomer, Arthur Eddington (1882-1944), exclaimed in 1933, “I feel almost an indignation that anyone should believe in it — except myself.” Why? Because “The beginning seems to present insuperable difficulties unless we agree to look on it as frankly supernatural.”

One team of astrophysicists (1973) opined that it “involves a certain metaphysical aspect which may be either appealing or revolting.” Robert Jastrow (1925-2008), head of NASA’s Goddard Institute for Space Studies, initially remarked, “On both scientific and philosophical grounds, the concept of an eternal Universe seems more acceptable than the concept of a transient Universe that springs into being suddenly, and then fades slowly into darkness.” And Templeton Prize winner (2011) Martin Rees recalls his mentor Dennis Sciama’s dogged commitment to an eternal universe, no-Big Bang model:

For him, as for its inventors, it had a deep philosophical appeal — the universe existed, from everlasting to everlasting, in a uniquely self-consistent state. When conflicting evidence emerged, Sciama therefore sought a loophole (even an unlikely seeming one) rather as a defense lawyer clutches at any argument to rebut the prosecution case.

Evidence forced theorists to abandon their preferred eternal-universe model. From the mid 1940s, Hoyle attempted to disprove the theory he named. Until 1964, when his preferred theory, the Steady State, lost an evidence test.

Here is a quick summary of some of the experimental evidence that emerged in the last few decades that caused naturalists to abandon the eternal universe that they loved so much when they were younger.

The importance of having a narrative

Now I want to make a very, very important point about Christianity and the progress of science. And that point is that it is very important that Christians present the evidence in exactly the way that Denyse presented it in that article – in its historical context, featuring the conflict between naturalists and the experimental evidence.

All Christians should be familiar with the following basic pieces of evidence which fit the war between science and naturalism narrative:

  1. The origin of the universe
  2. The cosmic fine-tuning
  3. The origin of life (biological information)
  4. The sudden origin of the Cambrian phyla
  5. The habitability/observability correlation

When you talk about these evidences as a Christian theist to non-Christians, you have to have cultivated a genuine interest in reconciling your beliefs with science. You have to accept that there are two books that reveal God’s character and attributes. The book of nature, and the book of Scripture. And you need to be flexible about getting these two books to fit together. The book of nature gives us natural theology (see Romans 1). It tells us that God is Creator and Designer. The book of Scripture tells us that God stepped into history as a man to save us by taking the punishment for our headlong rush away from God, which the Bible calls sin. Science is one way that humans can recover some of basic knowledge about God. Knowledge that is only possible because God created and designed the universe (and us) in such a way that we are capable of making discoveries, and that the universe is capable of being explored and understood.

It’s very important to present these five basic evidences to non-Christians in the historical context. And here is the story you must tell: “In the beginning, there was the naturalism, and the naturalism tried to argue from ignorance that God was not Creator and God was not Designer. And then came the science, and now people have to give up their naturalism in order to not be crazy and irrational”. That’s the narrative you use when talking to non-Christians about science.

In the beginning was the naturalism:

  1. In pre-scientific times, atheists maintained that the universe was eternal
  2. In pre-scientific times, atheists maintained that a life-permitting universe was as likely as a life-prohibiting universe
  3. In pre-scientific times, atheists maintained that the cell was a simple blob of jello that could spontaneously emerge in some warm pond
  4. In pre-scientific times, atheists maintained that the sudden origin of the Cambrian phyla would be explained by subsequent fossil discoveries
  5. In pre-scientific times, atheists maintained that there was nothing special about our galaxy, solar system, planet or moon

But then science progressed by doing experiments and making observations:

  1. Scientists discovered redshift and the cosmic microwave background radiation (evidence for a cosmic beginning) and more!
  2. Scientists discovered the fine-tuning of gravity and of the cosmological constant and more!
  3. Scientists discovered protein sequencing and exposed the myth of “junk DNA” and more!
  4. Scientists discovered an even shorter Cambrian explosion period and the absence of precursor fossils and more!
  5. Scientists discovered galactic habitable zones and circumstellar habitable zones and more!

And now rational people – people who want to have true beliefs about reality – need to abandon a false religion (naturalism).

Now naturally, science is in a state of flux and things change. But you have to look at the trend of discoveries, and those trends are clearly going against naturalism, and in favor of Christian theism. No one is arguing for a deductive proof here, we are simply looking at the evidence we have today and proportioning our belief to the concrete evidence we have today. People who are guided by reason should not seek to construct a worldview by leveraging speculations about future discoveries and mere possibilities. We should instead believe what is more probable than not. That’s what a rational seeker of truth ought to do. Proportion belief to probabilities based on current, concrete knowledge.

Atheism, as a worldview, is not rooted in an honest assessment about what science tells us about reality. Atheism is rooted in a religion: naturalism. And the troubling thing we learn from looking at the history of science is that this religion of naturalism is insulated from correction from the progress of science. Nothing that science reveals about nature seems to be able to put a dent in the religion of naturalism, at least for most atheists.

It falls to us Christian theists, then, to hold them accountable for their abuse and misrepresentation of science. And that means telling the story of the progress of science accurately, and accurately calling out the religion of naturalism for what it is – a religion rooted in blind faith and ignorance that has been repeatedly and convincingly falsified by the progress of science in the modern era.

Positive arguments for Christian theism

Nanotechnology expert Dr. James Tour assesses origin of life research

What is involved in creating life from non-life?
What is involved in creating life from non-life?

Recently, I watched lectures from a recent Science and Faith Conference that occurred at Park Cities Baptist Church in Dallas, Texas. I sent the lectures to my STEM women advisors to get their opinions. It was unanimous that Tour’s talk on origin of life research was the best. So let’s see his bio, then we’ll take a look at his lecture.

Dr. James Tour:

James M. Tour, a synthetic organic chemist, received his Bachelor of Science degree in chemistry from Syracuse University, his Ph.D. in synthetic organic and organometallic chemistry from Purdue University, and postdoctoral training in synthetic organic chemistry at the University of Wisconsin and Stanford University.

After spending 11 years on the faculty of the Department of Chemistry and Biochemistry at the University of South Carolina, he joined the Center for Nanoscale Science and Technology at Rice University in 1999 where he is presently the T. T. and W. F. Chao Professor of Chemistry, Professor of Computer Science, and Professor of Materials Science and NanoEngineering.

Tour’s scientific research areas include nanoelectronics, graphene electronics, silicon oxide electronics, carbon nanovectors for medical applications, green carbon research for enhanced oil recovery and environmentally friendly oil and gas extraction, graphene photovoltaics, carbon supercapacitors, lithium ion batteries, CO2 capture, water splitting to H2 and O2, water purification, carbon nanotube and graphene synthetic modifications, graphene oxide, carbon composites, hydrogen storage on nanoengineered carbon scaffolds, and synthesis of single-molecule nanomachines which includes molecular motors and nanocars.

[…]Tour has over 650 research publications and over 120 patents.

As he explains in the lecture, his research has frequently been used in the private sector to solve real world problems.

His lecture:

Evolution News had a short blurb of the lecture:

Rice University chemist James Tour almost defies description in a video now up of his amazing presentation at Discovery Institute’s 2019 Dallas Conference on Science and Faith.

At one point he asks for a show of hands of fellow synthetic chemists in the (large) audience. It turns out there are a couple and he demands that they stand up and call him a liar if anything he says isn’t true. His message is an alternatively scathing and hilarious indictment of claims from the origin-of-life studies community. Dr. Tour’s work in nanotechnology, an ulta-ultra-painstaking field, provides the backdrop for his demonstration that origins scientists don’t have the slightest idea how the first life was somehow naturally synthesized by blind, mindless forces.

The field hasn’t advanced an inch in 60-plus years. “Everyone’s clueless on this but no one wants to admit it.” Great scientists writing in the highest profile science journals are “lying to you” when they assert otherwise. “Show me the chemistry” of abiogenesis, he says. “It’s not there.”

Jim Tour is without parallel. Truly, I’d love to hear from our materialist critics how they would answer any of this.

At the conference, Tour’s lecture was accompanied by other great lectures on the origin of the universe and also the Cambrian explosion by Dr. Stephen C. Meyer. Jay Richards spoke on fine-tuning and habitability. You can find the links to those lectures on the Discovery Institute YouTube channel.

What we liked about the lecture by Dr. James Tour was that he did not dumb down the content for a church audience. I was sending screen captures of his slides and short video clips to my best friend Dina while I watched it. I was very excited to see someone so accomplished in his research and entrepreneurship being honest with the laypeople in the church. And I loved the church for letting him speak like a scientist. I didn’t understand everything he was saying about the science, but I always understood the point he was trying to make.

Let this lecture encourage to raise your children to focus on science, math, engineering and technology, because you can clearly see the value that we have in Dr. James Tour. We need hundreds more scientists who go to the best schools and make a difference.

I really hope that some of the younger Christians will understand the importance of making scientific evidence for a Creator and Designer more widely known. Learn the areas of science where God’s existence can be detected, and put the time in learning how to make those arguments.

Illustra Media videos on intelligent design are FREE to watch for 2 months

Hummingbird in flight
Hummingbird in flight

Sometimes Christian contact me through the blog and ask for advice on how to get their apologetics skills up. I usually send them a copy of “Is God Just a Human Invention?” and a set of 3 DVDs from Illustra Media. Well, Illustra Media decided to make ALL their DVDs FREE for the next 2 months. The videos cover topics about intelligent design (biology and physics) and evolution.

Here’s the blurb: (H/T Uncommon Descent)

During this period of uncertainty and massive change in the normal cycle of our daily routines, the Illustra Media staff, board of directors, and our distributor (RPI) want to offer encouragement and hope through the films we have produced during the past 20 years.

For the next 60 days, we will make streaming of our full length documentaries available free of charge. Click on any of the titles below to access the English versions. To stream international translations click here. You may bookmark this page for future reference. Please feel free to share it with your friends, family, and social media contacts throughout the world.

Here are the ones I’ve seen and recommend:

The first 3 are the ones that I send to Christian defenders in training. You can get them here from RPI. I’ve bought from him many times, and this is the best place to get them.

Unlocking the Mystery of Life is about design in the cell, biological information, irreducible complexity and molecular machines.

The Privileged Planet is about cosmic fine-tuning, habitability fine-tuning related to stars and planets, and discoverability.

Darwin’s Dilemma is about the sudden origin of new information for different body plans in the Cambrian explosion.

The other three are about interesting features of birds, butterflies, dolphins and whales that are obviously designed.

Notice how there is a video about birds, but no videos about cats. That is because cats are not very interesting, whereas birds are not only very interesting but also morally good – especially parrots and hummingbirds. My parents have a parrot who adjusts all his behavior to fit in with the family’s wishes, and he is even good when no one is around to watch him. They also have hummingbirds that come and hover around them to say hello, just because my parents put out feeders for them.

You can imagine in the past when early Christians would debate atheists, all their arguments were just holding up birds and saying “look at this obviously designed thing that speaks like a human, and it has such good moral character, too”. You can’t do that with evil cats, who probably did evolve from worms and slime by random mutations and natural selection. The early atheists probably just held up cats and argued that a morally good, all-powerful God would not create such awful things.

Anyway, here are some nice trailers for some of the videos that I like best:

Unlocking the Mystery of Life:

The Privileged Planet:

Darwin’s Dilemma:

Dolphins are pretty good!

Hummingbirds are the best!

I saved the best for last. They’re AWESOME!

Yale University computer science professor takes a look at protein formation probabilities

How did life begin?
How did life begin?

When I was in graduate school, we studied a book called “Mirror Worlds”, authored by famous computer science professor David Gelernter at Yale University. This week, I noticed that Dr. Gelernter had written an article in the prestigious Claremont Review of Books. In his article, he applies his knowledge of computer science to the problem of the origin of life.

Evolution, if it is going to work at all, has to explain the problem of how the basic building blocks of life – proteins – can emerge from non-living matter. It turns out that the problem of the origin of life is essentially a problem of information – of code. If the components of proteins are ordered properly, then the sequence folds up into a protein that has biological function. If the sequence is not good, then just like computer code, it won’t run.

Here’s Dr. Gelernter to explain:

How to make proteins is our first question. Proteins are chains: linear sequences of atom-groups, each bonded to the next. A protein molecule is based on a chain of amino acids; 150 elements is a “modest-sized” chain; the average is 250. Each link is chosen, ordinarily, from one of 20 amino acids. A chain of amino acids is a polypeptide—“peptide” being the type of chemical bond that joins one amino acid to the next. But this chain is only the starting point: chemical forces among the links make parts of the chain twist themselves into helices; others straighten out, and then, sometimes, jackknife repeatedly, like a carpenter’s rule, into flat sheets. Then the whole assemblage folds itself up like a complex sheet of origami paper. And the actual 3-D shape of the resulting molecule is (as I have said) important.

Imagine a 150-element protein as a chain of 150 beads, each bead chosen from 20 varieties. But: only certain chains will work. Only certain bead combinations will form themselves into stable, useful, well-shaped proteins.

So how hard is it to build a useful, well-shaped protein? Can you throw a bunch of amino acids together and assume that you will get something good? Or must you choose each element of the chain with painstaking care? It happens to be very hard to choose the right beads.

Gelernter decides to spot the Darwinist a random sequence of 150 elements. Now the task the Darwinist is to use random mutation to arrive at a sequence of 150 links that has biological function.

[W]hat are the chances that a random 150-link sequence will create such a protein? Nonsense sequences are essentially random. Mutations are random. Make random changes to a random sequence and you get another random sequence. So, close your eyes, make 150 random choices from your 20 bead boxes and string up your beads in the order in which you chose them. What are the odds that you will come up with a useful new protein?

[…]The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20150. In other words, many. 20150 roughly equals 10195, and there are only 1080 atoms in the universe.

What proportion of these many polypeptides are useful proteins? Douglas Axe did a series of experiments to estimate how many 150-long chains are capable of stable folds—of reaching the final step in the protein-creation process (the folding) and of holding their shapes long enough to be useful. (Axe is a distinguished biologist with five-star breeding: he was a graduate student at Caltech, then joined the Centre for Protein Engineering at Cambridge. The biologists whose work Meyer discusses are mainly first-rate Establishment scientists.) He estimated that, of all 150-link amino acid sequences, 1 in 1074 will be capable of folding into a stable protein. To say that your chances are 1 in 1074 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller. Axe puts them at 1 in 1077.

In other words: immense is so big, and tiny is so small, that neo-Darwinian evolution is—so far—a dead loss. Try to mutate your way from 150 links of gibberish to a working, useful protein and you are guaranteed to fail. Try it with ten mutations, a thousand, a million—you fail. The odds bury you. It can’t be done.

Keep in mind that you need many, many proteins in order to have even a simple living cell. (And that’s not even considering the problem of organizing the proteins into a system).

So, if you’re a naturalist, then your only resources to explain the origin of life are chance and mutation. As Dr. Gelernter shows, naturalistic explanations won’t work to solve even part of the problem. Not even with a long period of time.  Not even if you use the entire universe as one big primordial soup, and keep trying sequences for the history of the universe. It just isn’t possible to arrive at sequences that have biological function in the time available, using the resources available. The only viable explanation is that there is a computer scientist who wrote the code without using trial and error. Something that ordinary software engineers like myself and Dr. Gelernter do all the time. We know what kind of cause is adequate to explain functioning code.