BioLogos: New genetic information added

One of the arguments against evolution by natural selection is that information can only come from an intelligent agent. This article, in BioLogos, by Dennis Venema, refutes that assertion.

This article is not new, but it is important, and, after recently re-reading it, I wanted to call attention to it. It doesn't rule out divine activity, and, at the least, shows us, indirectly, that the God-produced systems of cellular biology are wonderfully complex, and have the power to bring about novel structures and molecules.

Thanks for reading.

Can evolution by natural selection be responsible for new information/new genes?

Last month, Stephen C. Meyer, an advocate for the Intelligent Design movement*, debated with two other persons.  I did not see, hear, or read the debate, but Meyer has posted about it, and Dennis Venema, of BioLogos, has also done so.

*Intelligent design is, in simplest terms, the idea that God planned the universe. The Intelligent Design movement, (ID) however, also believes this, but furthermore believes that God did not plan that natural selection would be capable of generating new information or new genes. ID also believes that it is possible to prove God's planning, and, by inference, His occasional intervention in living systems, scientifically, and that Intelligent Design should be taught as an alternative to evolution by natural selection in the public schools of the US. Some ID adherents also believe in a young earth. Some do not. I am not an IDer, but I do believe in intelligent design.

What was the debate about? Well, one thing that the debate was about was the question posed by the title. If the answer to that question is definitely shown to be "no," then ID gains considerable credibility. Not only that, but evolution by natural selection should not be taught in public (or private) schools as an explanation for the vast diversity of living things. Meyer believes that the answer is, indeed, no. He is wrong.

Why is he wrong?

One reason is that Meyer, and others, cite a paper by Douglas Axe. The paper was published in what I take to be a scientific, peer-reviewed, journal. Axe claims to have shown that the probability of protein being able to perform a new function is vanishingly small. However, there are some problems with Axe's work, or at least his conclusions. Some of them are detailed here. To summarize, Axe wasn't working with a normal protein, but with a chosen small subset of normal proteins. That means that his estimate of probability is too small. How much too small is impossible to state, but enough that it seriously weakens his argument. More criticism of the validity of using Axe's work to show that the answer to the question of the title of this post should be answered with a "no" is here.

The problem with Meyer's answer (and that of others) to the question is not only reliance on Axe. There is also a misunderstanding of probability. See here for more on that.

Dennis Venema argues, here, that the antibody-producing mechanism of vertebrates is, in fact, able, by natural means, to generate new DNA sequences, which can help defend against organisms, or substances, which have newly arisen. If the antibody-producing mechanism can do that, this shows that the answer to the question above is, at least partly, "yes."

Finally, what is probably the strongest argument that the answer to the question posed is, in fact, "yes," is that new genes have arisen within the recent past. One example of this is a gene in some bacteria which codes for a protein that allows them to use nylon as a food. (Nylon is a synthetic fiber which did not occur at all until the twentieth century.) That gene has arisen since the production of nylon, and its release into the environment. 

Another example of a new gene arising, in the recent past, is discussed here.  This post, discusses some posts by Venema, which describe another example of functional genetic material arising, apparently through natural selection.

It appears that part of God's design was the mechanism of natural selection, which makes it possible for natural systems to come up with new means of coping with new or unique environmental conditions. To me, and others, that is at least as amazing as it would be if God had, as it were, stepped in to specially create such solutions. 

Thanks for reading!

"We don't have a single example of a mutation resulting in a net gain of information. Not one" (But we do)

The title of this post quotes Eric Metaxas, and is part of a post, by him, on BreakPoint: "We don't have a single example of a mutation resulting in a net gain of information. Not one."

I appreciate Mr. Metaxas. I have read a couple of excellent books by him, and have previously posted about his writing, here and here. However, Mr. Metaxas, who has many gifts, and has done a great deal of good, is not an expert in genetics. He seems to be repeating a statement that he has heard from the Discovery Institute, an organization which argues that mutations did not bring about new functions in organisms. Please note that it is always possible to argue that any difference, however small, between two organisms is the result of God's specific miraculous intervention, and this cannot be experimentally disproved. (It has not been proved, either, and probably couldn't be, even if true.) But it can be doubted, and alternative mechanisms for the rise of new genetic information have been found.The Discovery Institute promotes the idea that God has, indeed, caused all changes in the DNA of two related species, because random changes cannot produce new functions. However, most scientists, Christian and otherwise, believe that most, or all, of such differences have come about through random mutation, followed by selection. Many Christian scientists believe that God has allowed random mutation and selection to exist, as a means of bringing about the diversity of organisms present on earth.

I'm not completely clear as to what Mr. Metaxas means by information. That is a complex subject, and different experts define it in different ways. But it seems clear that he is claiming that living things have never added a function as a result of a mutation. Sorry, but we do have such examples.

The first comment on Mr. Metaxas's post proposes that frameshift mutations have been a common means for the arrival of new functions, and provides a URL, which leads to this article, which is quite technical. The article claims that searching the genome of mice and humans has led to the discovery of several hundred genes that must have arisen by this type of mutation. The first two sentences of this article (after the abstract) are as follows:
"Several mechanisms, such as exon shuffling and alternative splicing, are responsible for novel gene functions, but they generate homologous domains and do not usually lead to drastic innovation. Major novelties can potentially be introduced by frameshift mutations and this idea can explain the creation of novel proteins."
The authors, then, believe that there are "several" mechanisms for the origin of novel gene functioning, including frameshift mutations.

The matter of the rise of new information has been discussed, in six posts in the BioLogos forum, by Dennis Venema. I briefly summarize these posts:
In the first, Venema discusses the position of the Discovery Institute, and the Intelligent Design Movement, and is related to the second paragraph of this post.
He says: "... describing how specified information can arise through natural means does not in any way imply God’s absence from the process. After all, natural processes are equally a manifestation of God’s activity as what one would call supernatural events."

In the second post, Venema describes the Long-Term Evolution Experiment. During this experiment, a colony of sexually reproducing bacteria experienced a mutation which allowed them to use citrate as an energy source, when, prior to that mutation, or series of mutations, they had not been able to do so.

In the third post, Venema discusses evidence that genes for hormone receptor proteins developed, in vertebrates, from duplication, and subsequent alteration, of an ancestral gene.

The fourth post argues, with evidence, that even the DNA responsible for complexly folded proteins may change so that a new function comes about, and that this has happened many times.

In his fifth post, Venema summarizes evidence that the entire vertebrate genome was duplicated, in an ancestor in the distant past, and that some of the "extra" copies of the genes thus formed have gone on to be responsible for new functions in vertebrates:
"This evidence is a strong indication that the modern vertebrate genome went through two rounds of [Whole Genome Duplication] early in its evolution, and that these events provided substantial 'raw material' for the acquisition of new information through gene divergence and neofunctionalization."

In his sixth, and last, post, Venema discusses the differences between the genes of humans and our closest relatives, the chimpanzees.

Thanks for reading. Mr. Venema, nor I, doubt that God is able to create, and change His creations, by any way He sees fit, including the miraculous. However we, and many other Christian scientists, believe that God designed the world so that random mutations, of various types, and natural selection, have given rise to much of the variety that is found in God's good creation. The assertion by Mr. Metaxas that forms the title of this post does not stand up the the evidence.

Added April 8, 2016: A later post on this blog refers to two other examples of recently arising functional genes.

describing how specified information can arise through natural means does not in any way imply God’s absence from the process. After all, natural processes are equally a manifestation of God’s activity as what one would call supernatural events. - See more at: https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/evolution-and-the-origin-of-biological-information-part-1-intelligent-design#sthash.baHk5Eyt.dpuf

describing how specified information can arise through natural means does not in any way imply God’s absence from the process. After all, natural processes are equally a manifestation of God’s activity as what one would call supernatural events. - See more at: https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/evolution-and-the-origin-of-biological-information-part-1-intelligent-design#sthash.baHk5Eyt.dpuf

What Todd Wood would like to hear an evolutionary creationist say, and what Dennis Venema would like to hear a young-earth creationist say

That's a long title!

I just found two interesting articles, both quite readable, and neither too long for the average reader who is interested in the subject, and neither requiring special background in science or theology. Both of these articles were written for the Colossian Forum.

Todd Charles Wood is a committed young-earth creationist, and a believer. He has sound scientific credentials. (See here for a summary of the information on him. I'm pretty sure that he is no longer at Bryan College, however. Here's his blog.) I have been reading his blog for a few years. He has written an article on what he would like to hear from an evolutionary creationist. Dennis Venema is a committed evolutionary creationist, and a believer. He has sound scientific credentials. (See here for a summary of the information on him. That link also leads to Venema's writing for the BioLogos Forum.) I have been reading his posts in the BioLogos Forum for a few years. He has written an article on what he would like to hear from a young-earth creationist.

So what do they say? Well you can, and should, read the articles. But I can sum it up simply -- each author admits that "his side" doesn't know everything, and should be properly humble about it, and understand that Christians may differ on some issues and still be Christians, and hopes that the representative of the other side will do the same. In the case of Venema and Wood, they have. Unfortunately, that is not always true, and Christianity is worse off because it isn't true.

We don't know everything about origins. We do know that God was involved. Thanks for reading. Read Wood and Venema.