Sometimes very active discussions about peripheral issues overwhelm a thread, so this is a permanent home for those conversations.
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Please use this thread for alerting admins to moderation issues and for discussion or complaints arising from particular decisions. This thread has been reissued as a post rather than a page as the “ignore commenter” button does not apply to threads started as pages.
In an early post John, who wants to be called doctor, urged readers to take a look at a little paper by Dan Nilsson and Suzanne Pilger. He says it is a good conceptual example of how natural selection acting on variation can gradually create a new feature.
Gee, that must be quite a paper. He says it can’t be beat! So what does their paper actually show? The paper is called , “A Pessimistic Estimate of the Time Required for an Eye to Evolve.” Well, that does sound interesting! Continue reading
So I wanted to write a post on the whole “density of functional proteins in amino acid sequence space” because, it seems to me, most ID proponents have some completely unwarranted beliefs about it. Recently it seems the main champion of the idea that evolving new protein functions would be so unlikely as to be practically impossible for evolution, even given several billion years, planet-spanning population sizes and natural selection, is Douglas Axe. He produced a paper in an (actual) peer reviewed journal back in 2004, and ID creationists have been spinning it ever since.
In 2007 a review of Axe 2004 appeared on Panda’s Thumb, by Arthur Hunt: Axe (2004) and the evolution of enzyme function. It recaps what Axe actually did and what he concluded from it, and I will add a bit about how it’s been pushed in ID circles since (see for example how it is pushed here: Imagine: 60 Million Proteins in One Cell Working Together.
This paper is interesting because it relates to the work of Douglas Axe that resulted in a paper in the Journal of Molecular Biology in 2004. Axe answered questions about this paper earlier this year, and also mentioned it in his recent book Undeniable (p. 54). In the paper, Axe estimated the prevalence of sequences that could fold into a functional shape by random combinations. It was already known that the functional space was a small fraction of sequence space, but Axe put a number on it based on his experience with random changes to an enzyme. He estimated that one in 10^74 sequences of 150 amino acids could fold and thereby perform some function — any function.
Evolutionists are fond of citing Orgel’s Second Rule: “Evolution is smarter than you are.” I have previously expressed skepticism about this rule (see here and here), but I’ve had no success in persuading people with a naturalistic metaphysical outlook. Yesterday, however, I came across a LiveScience article by Tia Glose titled, The Spooky Secret Behind Artificial Intelligence’s Incredible Power (October 9, 2016), which might prove to be a game-changer. We’ll see.
For those who have an interest.
Recently, I was browsing through the latest posts over at Evolution News and Views, and an anonymous article titled, Imagine: 60 Million Proteins in One Cell Working Together, caught my eye. By now, most readers at TSZ will be aware that I consider it overwhelmingly likely that the first living thing was designed. However, I’m also highly critical of attempts to over-egg the case for intelligent design. The article I read was one such attempt: it contained some unfortunate errors and omissions.
The physicist Arthur Zajonc provides us with his view of science that gives me hope for the future
Science can lead us away from reality into abstractions. It is too easy for the model to take over from the reality it is supposed to represent. The lived experience of the phenomenal world often takes a back seat. Zajonc gives us a couple of examples where the model dominates. The genetic code is one, and the neuroscience of the brain as a representative of the mind is another. If we are not careful our models become idols and the living reality is forgotten.
From a radio documentary featuring Arthur Zajonc he gives his views on Goethe’s science:
If you look at the actual practice that he undertakes it is I think faithful to the core principles of science, namely, it is empirically grounded, it proceeds from one methodical experience to the next, and it comes to a kind of insight, a moment of aperçu, of discovery.
He thinks that all good science proceeds in the way Goethe describes. It begins with insight. An example of which is Newton connecting a falling apple with the movement of the moon.
Continue reading
The basic biochemistry textbook I study from is Lehninger Prinicples of Biochemistry. It’s a well regarded college textbook. But there’s a minor problem regarding the book’s Granville-Sewell-like description of entropy:
The randomness or disorder of the components of a chemical system is expressed as entropy,
Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 23). W.H. Freeman. Kindle Edition.
Gag!
And from the textbook written by our very own Larry Moran:
In a recent post, keiths criticizes Alvin Plantinga’s Free Will theodicy, which (very briefly) goes as follows:
…[S]ome of the free creatures God created went wrong in the exercise of their freedom; this is the source of moral evil. The fact that free creatures sometimes go wrong, however, counts neither against God’s omnipotence nor against his goodness: for He could have forestalled the occurrence of moral evil only by removing the possibility of moral good.
(Plantinga, Alvin (1967). God and Other Minds. Ithaca, New York: Cornell University Press. Pages 166-167.)
Keiths responds:
Suppose God creates each person with free will, so that everything he or she does during life is freely chosen. If God is omniscient, he knows what all of those choices will be before the person is even created. If God simply chooses not to create the people who will go on to commit rape (or even experience the desire to commit rape), then he has prevented those things from happening without depriving anyone of their free will.
There are several things wrong with this reply. Continue reading
The ‘problem of evil’ is a perpetual thorn in the side of the omnitheist — that is, someone who believes in an omnipotent, omniscient, and omnibenevolent God. For if God is perfectly good and all-powerful, why does he allow so much evil in the world? He’s powerful enough to eradicate it; and if he’s perfectly good, he should want to eradicate it. So why doesn’t he?
One response, known as the ‘Free Will Defense’, comes from Alvin Plantinga:
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).
Continue reading
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.
1. Suicide?
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:
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.