For the past month or so I’ve been investigating the claim that the phylogenetic signal is evidence that a dataset shares common descent.
Supposedly, the phylogenetic signal is one of, if not the, strongest pieces of evidence for common descent. It is one of the first of the 29+ evidences for evolution offered over at Talk Origins (TO).
Quoting from the article:
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of “cladistic hierarchical structure” (also known as the “phylogenetic signal”) in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
I’ve been skeptical of this claim. A tree is just one kind of directed acyclic graph (DAG), and my hunch is many kinds of DAGs will also score highly on metrics for phylogenetic signal. I picked one metric, the consistency index (CI), which according to Klassen 1991 is the most widely used metric. It also is the featured metric in the above TO article. Plus, it is very simple to calculate. So, I’ve focused my efforts on the CI metric. Continue reading
In this series of videos Johannas Jaeger gives us some very interesting things to consider. He considers proteins to be pleomorphic assemblies not molecular machines.
Jaeger doesn’t believe in, nor feel the need to propose any extrinsic form of vitalism, but he does accept what Denis Walsh called methodological vitalism. If organisms are purposeful then it is an intrinsic purposefulness.
If we are to gain a meaningful understanding of the organism the machine metaphor will in no way suffice. Life is self-sustaining at all levels. The symbol of the caduceus is apt at so many levels, from the double helix of DNA to the movement of the solar system as it travels around the galaxy. Here is a link to a gif of the motion of the planets relative to the sun. Our hearts take on their form by the layers of muscle being laid down in a helical manner as the blood spirals onward. Continue reading
Nonlin.org has a burning desire to discuss sexual selection. So, let’s.
The topic was tangential (though not entirely unrelated) to the evolutionary psychology thread. Nonlin was unable to restrain his contempt for his interlocutors, and so his final missive was guanoed. The opportunity to repost was declined, as guanoing is ‘censorship’ (in plain sight!) and a ‘white flag’ allowing nonlin to declare victory and strut around like … well … a peacock.
This topic has recently come up in another thread & deserves its own thread, rather than getting lost there.
It started with KN asking CharlieM: “Are there really such ‘Darwinian extremists’ or are you just making them up?”
I responded: “The list of Darwinian extremists in SSH is considerable, not that it’s likely anyone here is even aware of this, such that they could come up with a list themselves.” http://theskepticalzone.com/wp/what-mixture-of-design-and-evolution-is-possible-as-the-idm-collapses/comment-page-24/#comment-279711
Left: The Annunciation by Henry Ossawa Tanner (1898). Philadelphia Museum of Art. Image courtesy of Wikipedia.
Right: Diorama of a Grey extra-terrestrial by G. W. Dodson, Roswell UFO Museum, Roswell, New Mexico, USA. Image courtesy of mr_t_77 from WV, USA and Wikipedia.
Let me begin with a confession. Temperamentally, I’m very much disposed to believing in angels – and aliens too, for that matter. I would certainly echo Hamlet’s famous saying, “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.” The notion that human beings are the most intelligent creatures in existence strikes me as a monstrous vanity.
Now, I don’t claim to know what other kinds of intelligences exist in our cosmos. But one thing I do know: both angels and aliens pose genuine conundrums for would-be defenders of the Christian faith. In a nutshell:
[For a brief explanation of my “An A-Z of Unanswered Objections to Christianity” series, and for the skeptical tone of this article, please see here. I’m starting my A-Z series with the letter H, and I’ll be zipping around the alphabet, in the coming weeks.]
In this article, I take aim at the Christian teaching that there was a special moment in history at which humans, who were made in the image of God, came into existence, and that a sharp line can be drawn between man and beast. I argue that on purely scientific grounds, it can be shown that such a view is highly unlikely. If the scientific arguments I put forward here are correct, then Christianity is in very big trouble.
The sinking of the Titanic, by Willy Stöwer, 1912.
During the past 25 years, there has been a dramatic resurgence in Christian apologetics, as many talented individuals have written books and given public speeches in defense of the Christian faith. Some of these people have even gone so far as to claim that we are now living in the Golden Age of Christian apologetics (see here, here and here). More books are being published than ever before, and the New Atheist movement, which appeared so powerful ten years ago, has largely fizzled out. The future looks good – or does it?
In this series, I’m going to explain in detail why I believe this rosy view is utterly mistaken, and why Christians are actually facing a thirty-year winter. Continue reading
Over at the “IDM collapse” thread I rather churlishly rejected CharlieM’s invitation to read an extensive piece by Stephen L. Talbott. Discovering he is a fan of Velikovsky did little to encourage me (that is, I fully realise, an argument from authority, but life is short and authors many. One needs a filter). What did catch my eye, however, is the fact that he is a contributor to Third Way of Evolution. This, on their front page, is what one might term their ‘manifesto’. Continue reading
This offers the simplest “neutral” colloquial mixture of “design” and “evolution” that I’ve seen in a long time. The site is no longer maintained, but the language persists.
“As a designer it is important to understand where design came from, how it developed, and who shaped its evolution. The more exposure you have to past, current and future design trends, styles and designers, the larger your problem-solving toolkit. The larger your toolkit, the more effective of a designer you can be.” http://www.designishistory.com/this-site/
Here, the term “evolution” as used just meant “history”. The author was not indicating “design theory evolution”, but rather instead the “history of designs” themselves, which have been already instantiated. Continue reading
Alan doesn’t believe that there are any other proposed explanations to rival ‘evolutionary theory’. At least none that so effectively account for the facts.
It is often said that there is no single theory of evolution, there are a group of mutually consistent theories. Be that as it may, I think we all understand the point Alan is making.
Evolution is a process whereby life has somehow emerged from a lifeless physical world and there is no overall teleology involved in its diversification. The reproductive processes produce a natural variety of forms which can take advantage of previously unoccupied niches. The basic sequence of events from primal to present are: lifeless minerals, water systems and gaseous atmosphere, followed by the arrival of simple prokaryote life forms, followed by multicellular organisms. Life is solely the product of physical and chemical processes acting on lifeless matter.
In this view life is nothing special, it just occurred because physical matter chanced to arrange itself in a particular way. And consciousness is just a by product of life.
But I suggest that there is an alternative way in which life as we perceive it could have come about.
Yesterday afternoon, acting on a recommendation by evolutionary biologist Jerry Coyne, I sat down and listened to a 43-minute Scientific American podcast featuring Stanford biology professor and hard determinist Robert Sapolsky being interviewed by Robert Mirsky, on the topic, “Your brain, free will and the law.” Suffice to say that I was underwhelmed. I had high expectations, as Professor Sapolsky is not only a well-published author (whose most recent work is Behave: The Biology of Humans at our Best and Worst), but also a professor of biological sciences, neurology and neurological sciences at Stanford University and a research associate at the National Museums of Kenya. I was both disappointed and amused with what I heard: disappointed with the complete absence of any rigorous argument against the existence of free will, and amused by the fake history related by Sapolsky, in the course of his interview with Robert Mirsky. By the way, for those readers who are looking for a critique of the doctrine of free will that’s both hard-hitting and substantive, I’d recommend the online writings of physicist Sabine Hossenfelder – in particular, her articles, How to live without free will, Free will is dead, let’s bury it and The Free Will Function: Free will from the perspective of a particle physicist (but see also the conclusion to her prize-winning 2018 essay, The Case for Strong Emergence, in which she acknowledges a gap in her argument). [Full disclosure here: I have previously critiqued Dr. Hossenfelder’s arguments against free will, and although I continue to find her case less than convincing, I would now acknowledge her general point that top-down causation alone won’t rescue free will.]
Back to Sapolsky. Since he’s a professor of biology, neurology and neurosurgery, I had hoped that he would at least attempt to summarize the biological case against free will, but he didn’t. He alluded to experiments by Benjamin Libet, noted in passing that there were multiple interpretations of these experiments, and then proceeded to his central argument: the “shrinking pie” argument, which relied on a very heavy dollop of fake history. In a nutshell: science has already shown that we are not responsible for X, Y and Z, so in time, science will show that we are not responsible for any of our actions. (By the way, Sapolsky is a hard determinist, who has no time for compatibilism and who eschews any notions of personal responsibility for our actions: as he puts it in his podcast, “We have no control, ultimately, over anything we do… We have no agency, and the criminal justice system does not make any sense at all.”)
So, what’s wrong with the “shrinking pie” argument? Everything.
A group of scientists and economists has devised a simple, tunable strategy for achieving exponential decrease in the number of new cases of Covid-19 while partially reopening the economy — or so it seems to me. The simplest form of the strategy is to alternate between consecutive days of work and consecutive days of lockdown. Although I am reluctant to add to the cacophony of inexpert opinions on how to deal with the pandemic, I will say that the strategy obviously works in an epidemiologic sense if the number of workdays per two-week cycle is sufficiently small. Furthermore, it is obvious that the number of workdays can be adjusted in response to the number of new cases. However, it is not obvious that can be set sufficiently high for the strategy to work in an economic sense. Modeling reported in the preprint “Cyclic Exit Strategies to Suppress COVID-19 and Allow Economic Activity” indicates that is likely to be sufficiently small. In other words, it seems that people might work half-time ( hours per two-week period) while driving the number of new cases toward zero. I am not qualified to judge epidemiological models, but will note that the results make sense if it is indeed the case that there is a “three-day delay on average between the time a person is infected and the time he or she can infect others.”
To be perfectly clear, I have not become a true believer in a strategy addressed in a preprint. I am saying that we should reject the notion that the pandemic will end only with herd immunity. It is not irrational to say that there may be, in the absence of an effective vaccination program, practicable methods of preventing most people from being infected, and that we should keep looking for them.
‘Stay the fuck home’. A less effective means of gaining general co-operation from the instinctively anti-establishment would be hard to imagine. How about you get the fuck out of my face? Our more formal UK government messaging has plumped for the ‘will-no-one-think-of-the-the-children’ emotional arm-twist of ‘Stay Home, Protect The NHS, Save Lives’. This appears at the foot of the rash of notices that has appeared all over my own rural region requesting people to approach a farm gate on a public path as they would open heart surgery, and disinfect or wear gloves before touching. After a day slapping cows’ backsides (I am hazy on the details of the profession!), it would be too much to expect farmers to take responsibility for their own biosecurity, and wash their own hands before dining.
We all know the story physical life has built up slowly on this earth. Its diversity now ranges from prokayotes to individuals possessing self-conscious creativity.
Out of those that believe in some form of evolution who would take issue with the very rough account that follows?
Life has its beginning in water. Multi-cellular life makes its appearance. The atmosphere changes in such a way as to allow animal life to evolve. Living creatures emerge from the water, moving over the land and breathing the air. At some point plants also spread out of the water and colonised the land. With animals came sentience and the development of individual consciousness. Possessing four limbs provided mobility while also allowing further development which gave a stable means of supporting the body. Organisms can then evolve in which these limbs are in a position to hold the body clear of the ground. Sentience develops to the stage where animals not only possess various sensations but they can also consciously communicate their inner feelings to others and make sense of the communication of others. The latest novel attributes of life are self consciousness and rational thinking. Humans not only communicate feelings but we can communicate objective thinking and are the most creative beings on the planet. We also have a modicum of free will which can be continuously developed over time. My account is beginning to contain details which, if people have any interest, a few might deem worth challenging.
Now it gets more controversial. Continue reading
[note: the author formatted this is a way that did not leave space for a page break. So I am inserting the break at the top — NR] Continue reading
The debate not only between Darwinists vs ID continues:
Are viruses dead or alive?
If viruses are dead, what makes them “animated”?
If viruses are alive, are they another life form?
Lehigh University biochemist and IDT spokesperson Dr. Michael Behe was recently asked by the Discovery Institute (DI) to write about covid-19. The following is to be found among what he wrote:
“do I think viruses were designed? Yes, I most certainly do! The viruses of which we are aware — including the coronaviruses, Ebola, and HIV — are exquisitely, purposively arranged, which is the clear signature of intelligent design [sic, properly “Intelligent Design”, since this “signature” is not being attributed to “strictly natural causes”]. Well, then does that mean the designer [sic, Divine Name = properly capitalized, “the Designer”] is evil and wants people to suffer? No, not necessarily. I’m a biochemist, not a philosopher. Nonetheless, I see no reason why a designer [sic, Divine Name = properly capitalized, “the Designer”] even of such things as viruses should be classified as bad on that basis alone.” – Michael Behe (10-03-2020, https://evolutionnews.org/2020/03/evolution-design-and-covid-19/
Behe concluded the article stating that he has “no reason to think either that viruses weren’t designed [meaning, by a Divine Designer] or that the designer [sic, Divine Name = properly capitalized, “the Designer”] of viruses isn’t good”.
I thought some of you might be interested to know that a paper of mine was recently published in BIO-Complexity – “Measuring Active Information in Biological Systems.” The goal of the paper is to provide a way of verifying whether (and how much) a mutational process is directed or undirected. I posted an overview of the paper at UD if you don’t have time to read it, but I thought this crowd might enjoy the details more.
Also, for background of why this is relevant, you might read my earlier paper, “Evolutionary Teleonomy as a Unifying Principle of the Extended Evolutionary Synthesis“.
I have been thinking about this. Who can one name, who is not in jail, and who would be eligible to be President, who would actually be worse than this moron, to lead the country through this crisis right now? Someone who is even more self-centered, who knows less about the world, less about proper management, who has had more business failures, who is even more divisive, who has more staffing problems, who is more petty, more insulting to reporters asking tough questions, and who generally would fuck things up even more than him? This is truly not an easy question to answer. Any suggestions? I am seriously finding it hard to name someone.
The republicans sure picked a doozy.