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

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

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.

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.

# Stephen C. Meyer and Marcus Ross lecture on the Cambrian explosion

Access Research Network is a group that produces recordings  of lectures and debates related to intelligent design. I noticed that on their Youtube channel they are releasing some of their older lectures and debates for FREE. So I decided to write a summary of one that I really like on the Cambrian explosion. This lecture features Dr. Stephen C. Meyer and Dr. Marcus Ross.

The lecture is about two hours. There are really nice slides with lots of illustrations to help you understand what the speakers are saying, even if you are not a scientist.

Here is a summary of the lecture from ARN:

The Cambrian explosion is a term often heard in origins debates, but seldom completely understood by the non-specialist. This lecture by Meyer and Ross is one of the best overviews available on the topic and clearly presents in verbal and pictorial summary the latest fossil data (including the recent finds from Chengjiang China). This lecture is based on a paper recently published by Meyer, Ross, Nelson and Chien “The Cambrian Explosion: Biology’s Big Bang” in Darwinism, Design and Public Education(2003, Michigan State University Press). This 80-page article includes 127 references and the book includes two additional appendices with 63 references documenting the current state of knowledge on the Cambrian explosion data.

The term Cambrian explosion describes the geologically sudden appearance of animals in the fossil record during the Cambrian period of geologic time. During this event, at least nineteen, and perhaps as many as thirty-five (of forty total) phyla made their first appearance on earth. Phyla constitute the highest biological categories in the animal kingdom, with each phylum exhibiting a unique architecture, blueprint, or structural body plan. The word explosion is used to communicate that fact that these life forms appear in an exceedingly narrow window of geologic time (no more than 5 million years). If the standard earth’s history is represented as a 100 yard football field, the Cambrian explosion would represent a four inch section of that field.

For a majority of earth’s life forms to appear so abruptly is completely contrary to the predictions of Neo-Darwinian and Punctuated Equilibrium evolutionary theory, including:

• the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phylum-level body plans;
• small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and
• a steady increase in the morphological distance between organic forms over time and, consequently, an overall steady increase in the number of phyla over time (taking into account factors such as extinction).

After reviewing how the evidence is completely contrary to evolutionary predictions, Meyer and Ross address three common objections: 1) the artifact hypothesis: Is the Cambrian explosion real?; 2) The Vendian Radiation (a late pre-Cambrian multicellular organism); and 3) the deep divergence hypothesis.

Finally Meyer and Ross argue why design is a better scientific explanation for the Cambrian explosion. They argue that this is not an argument from ignorance, but rather the best explanation of the evidence from our knowledge base of the world. We find in the fossil record distinctive features or hallmarks of designed systems, including:

• a quantum or discontinuous increase in specified complexity or information
• a top-down pattern of scale diversity
• the persistence of structural (or “morphological”) disparities between separate organizational systems; and
• the discrete or novel organizational body plans

When we encounter objects that manifest any of these several features and we know how they arose, we invariably find that a purposeful agent or intelligent designer played a causal role in their origin.

Recorded April 24, 2004. Approximately 2 hours including audience Q&A.

I learned a lot by watching great lectures from Access Research Network. Their YouTube channel is here. I recommend their origin of life lectures – I have watched the ones with Dean Kenyon and Charles Thaxton probably a dozen times each. Speaking as an engineer, you never get tired of seeing engineering principles applied to questions like the origin of life.

If you’d like to see Dr. Meyer defend his views in a debate with someone who reviewed his book about the Cambrian explosion, you can find that in this previous post.

Further study

The Cambrian explosion lecture above is a great intermediate-level lecture and will prepare you to be able to understand Dr. Meyer’s new book “Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design“. The Michigan State University book that Dr. Meyer mentions is called “Darwin, Design and Public Education“. That book is one of the two good collections on intelligent design published by academic university presses, the other one being from Cambridge University Press, and titled “Debating Design: From Darwin to DNA“. If you think this lecture is above your level of understanding, then be sure and check out the shorter and more up-to-date DVD “Darwin’s Dilemma“.