Yesterday, a couple of folks let me know of a paper that crypto-creationist [ETA: perhaps under reform] George Montañez had just posted at arXiv, “The Famine of Forte: Few Search Problems Greatly Favor Your Algorithm.” Below you’ll find my response to one of them. I should explain a few things, by way of introduction.
Montañez is a former advisee of the “Charles Darwin of intelligent design,” Baylor University professor Robert J. Marks II. Last I heard, he was pursuing doctoral studies in machine learning at Carnegie Mellon University. He worked not only with Marks, but also with William A. Dembski, the “Isaac Newton of information theory,” and Winston Ewert, the “Pooh Bear of evolutionary informatics,” on applications of measures of active information. He is still affiliated with them at the Evolutionary Informatics Lab. I refer to the core of affiliates who actually contribute to the output of the Lab — Marks, Dembski, Ewert, and Montañez — as Team EIL. The first three of them have a book scheduled for release by World Scientific on January 30, 2017. The title is Introduction to Evolutionary Informatics. I am trying to pull together a series of posts with the same title.
My email note follows.
[ETA: George Montañez has kindly responded here at TSZ. Contrary to what I guess below, he is not presently collaborating with the authors of the book.]
I just read, skimmed, struggled with Stephen Gould’s ” Structures of Evolution theory” Its really one long argument for Punctuated Equilibrium.
Aside from many interesting observations on the substance and style the surprising thing i note is how PE actually disproves all of evolutionary biology if you think about it. No wonder Dawkins and the rest smelled it as trouble and resisted. Wikipedia also resists it on this subject. Continue reading
In the ‘decisions’ thread walto made this comment:
‘Hard problem’? Hah! Piece of cake. Everything is instantiated! Well, you know what sorts of things can be instantiated? Look it up.
When I suggested that I’d not be doing that Mung noted:
Translation: don’t bother me with facts.
Which implies to me that there is a verified list of what can and cannot be instantiated in matter (chemicals and the like). I.E. Facts.
This is contrary to what I had originally assumed, hence my reluctance to bother looking it up. So I’ve changed my mind. I am interested in ‘looking it up’. I’m always willing to learn. So the floor is yours Mung, walto.
Dr. Joshua Swamidass, a theistic evolutionist, joined us recently at TSZ. I think the following comment of his will lead to some interesting and contentious discussion and is worthy of its own thread:
Third, if we drop “Darwinian” to just refer to the current modern synthesis of evolutionary theory, you are right that the scientific account does not find any evidence of direction or planning. I agree with you here and do not dispute this.
So the question becomes, really, is it possible that God could have created a process (like evolution) with a purposeful intent that science could not detect? I think the answer here is obvious. Of course He could. In fact, I would say, unless He wanted us to discern His purpose, we could not.
In my view, then, evolution has a purpose in creating us. Science itself cannot uncover its purpose. I find that out by other means.
Over at UD, pav posted a chart and claimed that it proves that AGW does not exist. Without getting into a discussion about AGW, I am interested to see if the theists here interpret this chart differently than the atheists. And if they do, why?
One of the most brilliant evolutionary biologists of the present day, Richard Sternberg, PhD PhD was ousted and permanently blacklisted by the National Institutes of Health and the Smithsonian Museum for his ID sympathies.
Sternberg is neither a Creationist nor Darwinist but classifies himself as a Process Structuralist which means he is not much involved in the ultimate questions of how things came to be, he just appreciates the amazing patterns of similarity and diversity in biology.
He was labelled by some of his former supporters as an intellectual terrorist after he used his position as editor of a journal to publish an ID-friendly article by Stephen Meyer in 2004. He paid dearly for that decision, and his subsequent dismissal from the NIH and Smithsonian precipitated special investigations by members of Congress and the White House a decade ago. Unfortunately, nothing of consequence was done for Sternberg and he was destroyed professionally and personally.
Despite his circumstances, he continued to publish excellent essays such as the one that highlights the non-random patterns of SINES (presumed by some to be junkDNA) which are present in mice and rats (link below).
ID is like the old locked room mysteries.
Scenario: Mr Body is found in a locked room with two bullet wounds in the back of his head. Lethal weapon found in his hand.
All the people known to profit from his death have airtight alibis. Security cameras show no one entering the room after Mr Body enters.
Only Mr Body’s fingerprints are found on the gun.
2. Magic or Divine Intervention?
3. Space Aliens having unknown technology?
4. Something else?
Interestingly, number one has actually been put forward in at least one actual, recent case.
If we substitute biogenesis for Mr Body’s death, ID proponents assume number two or number three.
If we substitute evolution for Mr Body’s Death, then Michael Behe and Mendel’s Accountant proponents assume number two or number three.
What do you guys think? What assumption do you think is most reasonable? I’m not asking what really happened. I’m asking what is the first working hypothesis that comes to mind?
The extent of variation present in human populations and the consequences of genetic load seem to be topics of perennial interest here (see, for example, recent comments in the Evolution Visualized thread). Recent issues of Nature have published a flurry of papers aimed at getting a better handle on just how much genetic diversity is likely to exist among humans. One notable paper from last August is the following:
In this study, Monkol Lek and many, many colleagues sequenced the exomes–i.e., the portion of DNA sequences that code for proteins along with some accompanying untranslated regions–of more than 60,000 people. The results were pretty spectacular. The paper is incredibly dense, but here are some highlights:
- The authors found more than 7 million reliably identified variants. Most were single base pair substitutions, but the variants also include more than 300,000 insertions/deletions.
- On average, 1 out of every 8 nucleotides is variable. However, the overwhelming majority of variants are rare. That is they are found in only a single or a few individuals
- The frequency of different kinds of variants is proportional to both the rate at which they occur as well as the extent to which they are likely to be deleterious. This is not at all surprising, but it’s neatly demonstrated. For example, 63.1% of all possible CpG transitions (i.e., a cytosine adjacent to a guanine that mutates to a thymine) were observed, while only 3% of possible transversions were present. CpG transitions are among the most common type of substitution in mammals, while transversions are less frequent. Likewise, the proportion of possible synonymous variants that were actually observed was much higher than the proportion of possible nonsynonymous variants that were observed, which is consistent with the generally accepted notion that nonsynonymous mutations are usually subject to stronger purify selection than synonymous mutations.
- They identified almost 180,000 different protein truncation variants (PTVs), which are protein-coding genes predicted to be shortened due to an introduced stop codon, a frameshift, or removal of a critical splice site. Amazingly (to me at least), the average genome in their dataset includes 85 PTVs in the heterozygous state and almost 35 PTVs in the homozygous state.
- They identified more than 100 variants previously thought to contribute to disease phenotypes that are present at anomalously high frequencies in human populations (> 1%). Based on the fact that the evidence of pathogenicity for most of these variants is actually extremely weak, the authors suggest that these variants are most likely benign.
There is a lot more in the paper that’s worth chewing over, so give it a read. This is easily the largest dataset of its type ever generated, but it has limitations. The sampling is heavily biased toward Europeans, and there is likely some variation missing, especially in Central and Middle Eastern Asia.
I imagine that within a few years, we’ll have datasets of similar size consisting of high-coverage, whole genome sequences, which will no doubt show even larger amounts of genomic variation. It’s an exciting time to be interested in biology!
In a recent comment, Fifthmonarchyman engaged with my accusation that his remarks on what brains can’t do is based on his ignorance of neuroscience. He responded by saying
it’s not about neuroscience it’s about ontology.
Brains don’t comprehend because they are not minds. I would think that someone so enamored with philosophy would have a handle on different categories of existence.
It is precisely as a philosopher that I want to express my complete rejection of the assumptions implicit in this remark.
I’ve written a genetic algorithm, which I have posted below, which implements single-step selection.
The relevant line for single-step selection is line 38:
fitness == 28 ? fitness : 0
- Have I successfully coded a genetic algorithm?
Is this a version of the Weasel program?
Does it demonstrate the power of cumulative selection?