Tag Archives: Evolution

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.

Atheist Jerry Coyne explains why morality is impossible for atheists

Sherlock Holmes and John Watson about to do philosophy
Sherlock Holmes and John Watson about to do philosophy

Let’s review what you need in your worldview in order to have a rationally grounded system of morality.

You need 5 things:

1) Objective moral values

There needs to be a way to distinguish what is good from what is bad. For example, the moral standard might specify that being kind to children is good, but torturing them for fun is bad. If the standard is purely subjective, then people could believe anything and each person would be justified in doing right in their own eyes. Even a “social contract” is just based on people’s opinions. So we need a standard that applies regardless of what people’s individual and collective opinions are.

2) Objective moral duties

Moral duties (moral obligations) refer to the actions that are obligatory based on the moral values defined in 1). Suppose we spot you 1) as an atheist. Why are you obligated to do the good thing, rather than the bad thing? To whom is this obligation owed? Why is rational for you to limit your actions based upon this obligation when it is against your self-interest? Why let other people’s expectations decide what is good for you, especially if you can avoid the consequences of their disapproval?

3) Moral accountability

Suppose we spot you 1) and 2) as an atheist. What difference does it make to you if you just go ahead and disregard your moral obligations to whomever? Is there any reward or punishment for your choice to do right or do wrong? What’s in it for you?

4) Free will

In order for agents to make free moral choices, they must be able to act or abstain from acting by exercising their free will. If there is no free will, then moral choices are impossible. If there are no moral choices, then no one can be held responsible for anything they do. If there is no moral responsibility, then there can be no praise and blame. But then it becomes impossible to praise any action as good or evil.

5) Ultimate significance

Finally, beyond the concept of reward and punishment in 3), we can also ask the question “what does it matter?”. Suppose you do live a good life and you get a reward: 1000 chocolate sundaes. And when you’ve finished eating them, you die for real and that’s the end. In other words, the reward is satisfying, but not really meaningful, ultimately. It’s hard to see how moral actions can be meaningful, ultimately, unless their consequences last on into the future.

Theism rationally grounds all 5 of these. Atheism cannot ground any of them.

Let’s take a look at #4: free will and see how atheism deals with that.

Atheism and free will?

Here’s prominent atheist Jerry Coyne’s editorial in USA Today to explain why atheists can’t ground free will. (Note: link is dead)

Excerpt:

And that’s what neurobiology is telling us: Our brains are simply meat computers that, like real computers, are programmed by our genes and experiences to convert an array of inputs into a predetermined output. Recent experiments involving brain scans show that when a subject “decides” to push a button on the left or right side of a computer, the choice can be predicted by brain activity at least seven seconds before the subject is consciously aware of having made it. (These studies use crude imaging techniques based on blood flow, and I suspect that future understanding of the brain will allow us to predict many of our decisions far earlier than seven seconds in advance.) “Decisions” made like that aren’t conscious ones. And if our choices are unconscious, with some determined well before the moment we think we’ve made them, then we don’t have free will in any meaningful sense.

If you don’t have free will, then you can’t make moral choices, and you can’t be held morally responsible. No free will means no morality.

Here are some more atheists to explain how atheists view morality.

William Provine says atheists have no free will, no moral accountability and no moral significance:

Let me summarize my views on what modern evolutionary biology tells us loud and clear — and these are basically Darwin’s views. 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.

Richard Dawkins says atheists have no objective moral standards:

In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won’t find any rhyme or reason in it, or any justice. The universe that we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference… DNA neither knows nor cares. DNA just is. And we dance to its music. (Richard Dawkins, River Out of Eden: A Darwinian View of Life (1995))

When village atheists talk about how they can be moral without God, it’s important to ask them to justify the minimum requirements for rational morality. Atheists may act inconsistently with their worldview, believing in free will, expecting praise and blame for complying with the arbitrary standards of their peer group, etc. But there is nothing more to morality on atheism that imitating the herd – at least when the herd is around to watch them. And when the herd loses its Judeo-Christian foundation – watch out. That’s when the real atheism comes out – the atheism that we’ve seen before in countries that turned their backs on God, and the moral law. When God disappears from a society, anything is permissible.

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.

Stephen C. Meyer lectures on intelligent design and the origin of life

Christianity and the progress of science
Christianity and the progress of science

A MUST-SEE lecture based on Dr. Stephen C. Meyer’s book “Signature in the Cell“.

I highly recommend watching the lecture, and looking at the slides. The quality of the video and the content is first class. There is some Q&A (9 minutes) at the end of the lecture.

Topics:

  • intelligent design is concerned with measuring the information-creating capabilities of natural forces like mutation and selection
  • Darwinists think that random mutations and natural selection can explain the origin and diversification of living systems
  • Darwinian mechanisms are capable of explaining small-scale adaptive changes within types of organisms
  • but there is skepticism, even among naturalists, that Darwinian mechanisms can explain the origin of animal designs
  • even if you concede that Darwinism can account for all of the basic animal body plans, there is still the problem of life’s origin
  • can Darwinian mechanisms explain the origin of the first life? Is there a good naturalistic hypothesis to explain it?
  • there are at least two places in the history of life where new information is needed: origin of life, and Cambrian explosion
  • overview of the structure of DNA and protein synthesis (he has helpful pictures and he uses the snap lock blocks, too)
  • the DNA molecule is composed of a sequence of bases that code for proteins, and the sequence is carefully selected to have biological function
  • meaningful sequences of things like computer code, English sentences, etc. require an adequate cause
  • it is very hard to arrive at a meaningful sequence of a non-trivial length by randomly picking symbols/letters
  • although any random sequence of letters is improbable, the vast majority of sequences are gibberish/non-compiling code
  • similarly, most random sequences of amino acids are lab-proven (Doug Axe’s work) to be non-functional gibberish
  • the research showing this was conducted at Cambridge University and published in the Journal of Molecular Biology
  • so, random mutation cannot explain the origin of the first living cell
  • however, even natural selection coupled with random mutation cannot explain the first living cell
  • there must already be replication in order for mutation and selection to work, so they can’t explain the first replicator
  • but the origin of life is the origin of the first replicator – there is no replication prior to the first replicator
  • the information in the first replicator cannot be explained by law, such as by chemical bonding affinities
  • the amino acids are attached like magnetic letters on a refrigerator
  • the magnetic force sticks the letters ON the fridge, but they don’t determine the specific sequence of the letters
  • if laws did determine the sequence of letters, then the sequences would be repetitive
  • the three materialist explanations – chance alone, chance and law, law alone – are not adequate to explain the effect
  • the best explanation is that an intelligent cause is responsible for the biological explanation in the first replicator
  • we know that intelligent causes can produce functional sequences of information, e.g. – English, Java code
  • the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein
A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone
Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Positive arguments for Christian theism

William Lane Craig debates Austin Dacey: Does God Exist?

Two tough rams butt heads, and may the best ram win!
Two tough rams butt heads, and may the best ram win!

Here is the video and summary of a debate between Christian theist William Lane Craig and Austin Dacey at Purdue University in 2004 about the existence of God.

The debaters:

The video: (2 hours)

The video shows the speakers and powerpoint slides of their arguments. Austin Dacey is one of the top atheist debaters, and I would put him second to Peter Millican alone, with Walter Sinnott-Armstrong in third place. This is the debate to show people who are new to apologetics. The debate with Peter Millican is better for advanced students, and that’s no surprise since he teaches at Oxford University and is familiar with all of Dr. Craig’s work. The Craig-Dacey debate is the one that I give to my co-workers.

By the way, you can get the DVDs and CDs for the first Craig-Dacey debate and the second Craig-Dacey debate and the second Craig-Sinnott-Armstrong debate. The Peter Millican debate is not available on DVD, but the link above (Peter Millican) has the video and my summary.

Dr. Dacey’s 5 arguments below are all good arguments that you find in the academic literature. He is also an effective and engaging speaker, This is a great debate to watch!

SUMMARY of the opening speeches:

Dr. Craig’s opening statement:

Dr. Craig will present six reasons why God exists:

  1. (Contingency argument) God is the best explanation of why something exists rather than nothing
  2. (Cosmological argument)  God’s existence is implied by the origin of the universe
  3. (Fine-tuning argument) The fine-tuning of the universe for intelligent life points to a designer of the cosmos
  4. (Moral argument) God is the best explanation for the existence of objective moral values and objective moral duties
  5. (Miracles argument) The historical facts surrounding the life, death and resurrection of Jesus
  6. (Religious experience) God’s existence is directly knowable even apart from arguments

Dr. Dacey’s opening argument:

There are two ways to disprove God’s existence, by showing that the concept of God is self-contradictory, or by showing that certain facts about ourselves and the world are incompatible with what we would expect to be true if God did exist. Dr. Dacey will focus on the second kind of argument.

  1. The hiddenness of God
  2. The success of science in explaining nature without needing a supernatural agency
  3. The dependence of mind on physical processes in the brain
  4. Naturalistic evolution
  5. The existence of gratuitous / pointless evil and suffering

One final point:

One thing that I have to point out is that Dr. Dacey quotes Brian Greene during the debate to counter Dr. Craig’s cosmological argument. Dr. Craig could not respond because he can’t see the context of the quote. However, Dr. Craig had a rematch with Dr. Dacey where was able to read the context of the quote and defuse Dr. Dacey’s objection. This is what he wrote in his August 2005 newsletter after the re-match:

The following week, I was off an another three-day trip, this time to California State University at Fresno. As part of a week of campus outreach the Veritas Forum scheduled a debate on the existence of God between me and Austin Dacey, whom I had debated last spring at Purdue University. In preparation for the rematch I adopted two strategies: (1) Since Dacey had come to the Purdue debate with prepared speeches, I decided to throw him for a loop by offering a different set of arguments for God, so that his canned objections wouldn’t apply. I chose to focus on the cosmological argument, giving four separate arguments for the beginning of the universe, and on the evidence for Jesus’ resurrection. (2) I reviewed our previous debate carefully, preparing critiques of his five atheistic arguments. In the process I found that he had seriously misunderstood or misrepresented a statement by a scientist on the Big Bang; so I brought along the book itself in case Dacey quoted this source again. I figured he might change his arguments just as I was doing; but I wanted to be ready in case he used his old arguments again.

[…]The auditorium was packed that night for the debate, and I later learned that there were overflow rooms, too. To my surprise Dr. Dacey gave the very same case he had presented at Purdue; so he really got clobbered on those arguments. Because he wasn’t prepared for my new arguments, he didn’t even respond to two of my arguments for the beginning of the universe, though he did a credible job responding to the others. I was pleased when he attacked the Big Bang by quoting the same scientist as before, because I then held up the book, specified the page number, and proceeded to quote the context to show what the scientist really meant.

Dr. Craig is always prepared!