Bill Cole's Case For Design

Aside from the politics they have identified the only known mechanism that can create a functional sequence of any length reliably. Conscious intelligence. The functional sequence problem is mission critical to understanding how organisms evolved or were specially created.


I think you’re exactly right but what experiment supports how genomes change and gain function? If bacteria can’t gain function through reproduction how do you explain the eukaryotic cell from an evolutionary perspective?

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The problem is that no one has shown FI is necessary to produce the biodiversity we see today. FI can’t be measured quantitatively, so there is no way of determining if it has increased or decreased after a mutation.

If you think I am wrong, then I would suggest a simple experiment. Google for a random DNA sequence generator and start with something smallish, like a 5k base pair random sequence. Measure the functional information in that sequence. Next, make 10 random mutations to that sequence and remeasure the FI and see if it has increased or decreased. I would be interested in seeing the actual numbers.

From what I have read, natural genetic engineering is just random mutations (with respect to fitness) and natural selection.

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We know that random changes to FI (DNA) can cause fatality and the scientific literature is filled with these type of mutations. It is a fair assumption if the organism dies after a mutation it has lost information.

We also know that FI can be preserved over deep evolutionary time as measured by sequence preservation by animals who’s ancestors have large age differences.

We know that the DNA repair mechanism is critical for life and mutations to it can cause disease.

We know that the diversity of life correlates with different DNA sequences.

We now that enzymes will not function if we make enough changes to their sequence.

We know that similar functional sequences will reliably create animals that look like each other.

Functional information is real and critical for living organisms. Function lives in very large mathematical space so statistically it will degrade with random change.

Just because some mutations are lethal does not mean all of them are. Humans and chimps differ by about 40 million mutations, and it is pretty obvious that those are not lethal mutations. We also know that those mutations are responsible for the beneficial adaptations in both species. If that is not an increase in FI, then FI is meaningless.


Read Shapiro’s book Evolution for the 21st century. NGE is about extrapolating deterministic genetic changes that are observed like gene reshuffling. The basis is the work of Nobel prize winner Barbara McLintock.
Shapiro believes that deterministic changes are required to gain function. This is the only rational position IMO.

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In each of the cases I have read it is still random mutation. Gene reshuffling results in deleterious, neutral, and beneficial changes which makes it random with respect to fitness.


I did not make the claim that all of them are. If some are then that is evidence sequence matters. How do you know the cause of the 40 million mutations you are observing?

You don’t know that these changes are responsible for all the morphological differences. Gene expression patterns are different and alternative splicing patterns are different you need to isolate the cause of these differences.

You also don’t know the cause of the DNA differences. You are assuming they are near neutral or neutral mutations.

Does it even make sense that a human can be created with 40 million random near neutral mutations? Josh said he cannot eliminate guidance as a cause. What do you think?

Because the bias of mutations is consistent with observed mechanisms of mutagenesis. Specifically, there is a bias towards transitions and CpG mutations. You can read all about it in a wonderful essay written by @glipsnort found here:

The differences in gene expression are due to differences in DNA sequence, and the same applies to alternative splicing patterns. Identical genomes will have identical gene expression patterns in response to the same stimuli. The only way you get differences in gene expression and splicing is through a difference in primary DNA sequence.

See the essay above. The evidence clearly points to the observed mechanisms of mutagenesis seen in modern life.

No such assumption is being made. If the vast majority of a genome shows no sign of sequence conservation then this is strong evidence that the vast majority of mutations will occur in regions where they are neutral. The percentage of neutral mutations will depend on which genome we are talking about. In the case of humans, about 90% of the human genome shows no evidence of sequence conservation so at least 90% of mutations will be neutral.

Since the evidence is consistent with the majority of the 40 million mutations being neutral, then that is the evidence I follow.

So I assume you can identify the DNA changes that caused these changes?

There’s that sleight of hand parlor trick.

You are describing things, as if the whole purpose is to generate a particular DNA sequence. But, from the point of view of the organism and population, the purpose is to survive in a changing environment. And, as its set of tools, the population has the ability to produce mutations and do trial and error testing to see which best help survival.

Suppose that Lenski, after he saw that unexpected mutation, had changed his experiment. Suppose he threw away his experimental populations other than the one where the mutation occurred. Then he split that population to form a new experiment. And maybe he changed the chemicals used, varying them between the different test tubes. And then, after another mutation was observed, he again modified the experiment. Via that process, he would get a new DNA sequence.

You would probably complain that Lenski had designed that new DNA sequence with the variations in his experiment. And I would agree with that. But the point is that there is already a great deal variation in the environment – enough variation to drive the evolutionary changes that we observe.

The response of the population, using genetic change (mutation) with trial and error testing, is an example of natural intelligence. But the ID proponents don’t see that. We might say that the naturally occurring intelligence is hidden in plain view. But it isn’t conscious, so the people looking for conscious intelligence cannot see it.

The paper you attached is very interesting. Thank you. I will spend some time with it.

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It’s basic genetics. If the sequence is the same then gene expression is the same. One example is human specific duplication mutations for the notch family of genes as it relates to human brain development:

Added in edit:

The reason that identical twins look identical is that their genomes are identical. Same sequence, same gene expression. Same gene expression, same embryonic development.

Neil you are a math guy. The change has to be deterministic. The environment is changing a sequence by mutation which is random. The only possible outcome here is bad with any sustained length of trials.

If we weren’t observing a sequence I would agree you that you have a case.

No, this is false. Gene expression is not controlled by DNA alone.

I completely agree. Gene expression can be affected by changes in the environment. However, identical sequences will have the same shift in gene expression when exposed to the same environmental stimuli. I have personally measured changes in gene expression, so I am fully aware of the basics of this process.

Here is something else to consider. If gene expression is not tied to DNA sequence then life as we know it wouldn’t work. Tissues in your body are groups of cells that serve the same function, and they act in a similar fashion because they have the same DNA. If gene expression could change willy nilly without any connection to DNA sequence then your body wouldn’t work. You would be a big mush of cells all doing different things.

Where is the math to back this up? The 40 million mutations separating humans and chimps seems to be telling an entirely different story, not to mention the mutations that separate any two species. If genomes can’t be changed then there would only one species made up of individuals with identical genomes.


It is a very different statement to say the gene expression is tied to DNA and that we can determine gene expression by DNA alone. We cannot necessary understand the splicing differences and gene expression differences by observing mutations or changes to DNA.

The next step in the paper you cited on mutational comparison is to see what those mutations are doing. I would expect the patterns he is showing because time creates mutational variation but we know there is redundancy in DNA from the genetic code and the number of coded amino acids. So now you need to extract the signal from the noise. Neutral mutations vs mutations that effect morphological change.

This is the problem that needs to be reconciled. I would suggest you don’t discount guidance so quickly.

I keep reiterating that the environment plays a role, so please don’t forget that. For instance, I have meausred IL-6 expression in immune cells after exposure to lipopolysacchride, and I can tell you that the environment makes a huge difference.

One good example of what I am talking about is adult lactose tolerance. This is due to mutations upstream of the lactase gene which allows its expression to continue through adulthood instead of being shut down in childhood.

Let’s first see if we have agreement on the first step. Do you agree that the evidence presented in the article supports mutations as the source of variation between species?

The next basic question you need address is why you think humans and chimps are physically different from each other. Is it due to different DNA sequences in their respective genomes? If not, how do you explain those physical differences?