What’s wrong with this paper?

Taking a new tack with the common descent/common design theme, I’d like to sneak up on it. As Sal Cordova likes to do, I offer a hypothesis for critique. Here’s an old phyogenetic analysis of mine. Does it show common descent? If not, what’s wrong with it?

Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003;  52:386-402.

This one is about crocodiles. Are crocodiles all the same kind? How do you know? If they aren’t how many kinds are there within the group and how do you know? If they are, are they a whole kind or just part of a larger kind? And if the latter, what is the larger kind?

Craniopagus twins revisited: A response to Professor Egnor

Professor Michael Egnor has kindly responded to my post, The craniopagus twins from British Columbia: A test case for Thomistic dualism (TSZ, November 25, 2017), in a new post, titled, The Craniopagus Twins and Thomistic Dualism (ENV, December 10, 2017). In my earlier post, I had argued that “the twins’ ability to share thoughts without speaking weakens the case for Thomistic dualism, and lends support to a subtle variety of materialism which incorporates top-down causation.” In his response, Professor Michael Egnor gets to the heart of our disagreement and explains why he does not think that the experiment I proposed would serve to test whether dualism or materialism is true. Egnor proposes another test of his own, relating to mathematical abilities. In this post, I’d like to explain why I object to Professor Egnor’s test, before putting forward another one, very similar to it, which I believe could experimentally resolve whether dualism or materialism is true. Finally, I offer a few reflections on the philosophical argument which, Egnor contends, makes materialism logically untenable.

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At last, an intelligent solution to the problem of global warming

Sequestration of carbon dioxide emissions from a thermal power plant

I’d like to draw readers’ attention to an excellent article in Quartz magazine (December 4, 2017) by Akshat Rathi, titled, Humanity’s fight against climate change is failing. One technology can change that. Dr. Rathi has a Ph.D. in chemistry from Oxford, and his article is based on lengthy conversations with more than 100 academics, entrepreneurs, policy experts, and government officials.

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The Fine-Tuning Argument – Kettle Logic on a Cosmological Scale

As a relatively recent arrival here at TSZ, I am somewhat intrigued to still see the Fine-Tuning Argument in regular rotation.  It appears often in comments, but the two most recent OP’s that I have come across dedicated to the topic are Mung’s ‘The Wonder of Water‘ and RobC’s ‘The Big Numbers Game‘.

That I find the Fine-Tuning Argument completely unconvincing will not come as a surprise to anyone who has read any of my comments on TSZ.  But I think it is worth taking a moment to explain why that is as my reasoning differs slightly from that of others whose comments I have seen.  In a comment on the ‘Wonder of Water’ thread, Joe Felsenstein comes closest while referring to the ability of the Schrodinger Wave Equation to model all of the properties that we see expressed in Chemistry:

“If Michael Denton’s Intelligent Designer wants to fine-tune properties of water she has to do it by tinkering with the SWE. Which would mess up a lot else.”

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Two-million-year-old Adam and Eve still possible: Dr. Ann Gauger’s model remains viable

A few weeks ago, I wrote a short post titled, Adam and Eve still a possibility?, in which I drew readers’ attention to the work of geneticist Richard Buggs, Reader in Evolutionary Genomics at Queen Mary University of London, who thinks it’s still theoretically possible that the human race once passed through a short, sharp population bottleneck of just two individuals, followed by exponential population growth. Biologist Dennis Venema, professor of biology at Trinity Western University in Langley, British Columbia, has recently written a two-part reply to Buggs, titled, Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1) and A Reply to Dr. Richard Buggs (Part 2). But in a comment in response to a query of mine, Professor Venema conceded that at the present time, science cannot rule out Dr. Ann Gauger’s hypothesis that there was a severe bottleneck around two million years ago, with the emergence of Homo erectus, whom she identifies as the first true human being. When I pressed Professor Venema, saying, “In plain English, what you’re saying is that science can’t rule out an original couple, if they lived more than 1 million years ago,” he replied:

I guess it depends on how reliable you think PSMC methods are as they approach this time frame. The data looks smooth to me out to around 1.5 MYA or so, plus or minus, but the method loses its power as you go back further and further.

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Naturalism Without Mechanism

As there is occasional interest in the relation between science and metaphysics here, I thought I’d share this article: “Metaphysics of Metamorphosis“, by the philosopher of science John Dupre. Dupre argues that metaphysics that takes science seriously — what he calls “naturalistic metaphysics” — will give us a very different picture of reality than what we get from traditional a priori metaphysics:

This project of science-based metaphysics, sometimes referred to as ‘naturalistic metaphysics’, has been surprisingly controversial. The philosophers James Ladyman at the University of Bristol and Don Ross at the University of Cape Town offered a forceful defence in their book Every Thing Must Go (2007). As that book illustrates, the debate can be technical and vitriolic. Consequently, I won’t defend naturalistic metaphysics from its critics so much as show you how it helps us inch towards an answer to one of the oldest chestnuts in the history of philosophy: is reality made up of things that somehow change over time, or are things just temporary shapes that our perception plucks out from a flux of unruly, unfolding processes?

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The craniopagus twins from British Columbia: A test case for Thomistic dualism

The story of Krista and Tatiana Hogan, 11-year-old twin girls born in Vancouver, British Columbia, who are joined at the top, back, and sides of their heads, will doubtless be familiar to most readers. Here’s a documentary that was made about the twins:

Over at Uncommon Descent and Evolution News and Views, Denyse O’Leary, David Klinghoffer and Michael Egnor (who is a Professor of Neurosurgery at State University of New York, Stony Brook), have argued that the Hogan twins constitute a living refutation of the materialistic notion that mind and brain are one and the same thing. Each twin has her own distinct mind and personality, despite the fact that they share parts of their brains.

In this post, I’m going to argue that while these three authors are perfectly correct in insisting that each twin does indeed possess a mind of her own, their claim that this fact refutes materialism is profoundly mistaken. On the contrary, I will argue that the twins’ ability to share thoughts without speaking weakens the case for Thomistic dualism, and lends support to a subtle variety of materialism which incorporates top-down causation. And on this point, the mother of the Hogan twins would probably agree with me: she sends her children to a school run by the Seventh-day Adventist Church, which teaches that the human brain is the seat of thought, language, creativity, morality and even our consciousness of God. Could this Christian version of materialism be correct, after all?

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Defining Fitness

There is a pretty interesting discussion going on in Noyau regarding the many definitions of “fitness” in evolutionary biology. It would be a shame for it to be lost in that particular venue here at TSZ. At the risk of being censored by the admins for posting too many OPs in one month I thought I’d start this thread.

Here’s my take so far:

Allan Miller was charged by phoodoo with resorting to different definitions of fitness. Allan denied the charge and when asked for a definition of fitness Allan provided one. Allan later stated that his definition only properly applied to asexual species.

Others chimed in to say that the definition of fitness depends on the context, which hardly seems to contradict what phoodoo was saying.

My own position is that fitness has its definition within a particular mathematical framework. My position is also that fitness can be defined generically but that such a definition is tautological. Special definitions of fitness are required to make the concept testable.

Here’s hoping we can move the discussion about fitness out of Noyau.

Not-so-intelligent design

Much of the popular debate about evolution is between neo-Darwinians and neo-Paleyans (advocates of “intelligent design”). If you ask a neo-Paleyan who the intelligent designer is, they typically say they believe “God”, but there are other possible answers, for example, “extraterrestrials”, which begs the question “Who designed extraterrestrials?”, although I will ignore it. Continue reading

Five Questions Everyone Should Ask about Common Descent

I received my copy of Theistic Evolution today. The book contains three chapters dedicated to skepticism of universal common ancestry. As common descent seems to be a hot topic here lately I thought I’d read those chapters first and offer comments and invite responses.

I’ll start with Chapter 12, authored by Paul Nelson, which carries the title: Five Questions Everyone Should Ask about Common Descent. The five questions are as follows:

1. If species were not connected by common descent, how would we know it?
2. What were the actual transformation pathways, satisfying the continuity rule, which connect all organisms to LUCA?
3. Have we genuinely tested UCD, or merely assumed its truth?
4. When explaining the history of life, have we assumed methodological naturalism only, or have we allowed for the possibility of intelligent design?
5. In the light of intelligent design as a causal possibility, what histories for life on earth might be the case?

As usual, I don’t expect anyone else here to actually read this book because, you know, it just isn’t skeptical enough.

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The Ills of the Skeptical Movement

In another post, recent contributor TomMueller stated that GPS satellites use relativistic synchronization to match up their clocks with earthbound clocks.  I explained to him that this was not so, even though its easy to believe, if you don’t think critically, that it is.

Tom followed my post to him with a litany of ad hominem, “Oh, you are a moron, you are a troll, creationist idiots,  I read about it on a credible site, I talked to a physics professor about it…” and on and on he went with his insults and denial.

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Can Evolution be possible if Entropy is true; or rather, is Evolution possible because Entropy is true!

So what is Entropy?

To follow in the tradition of Maimonides. Entropy is NOT a tendency to disorder! I need to thank Joe Felsenstein for directing me to Frank L. Lambert’s insights on a previous thread probably best left alone. Here is a great site to elucidate Lambert’s insights:


What about Evolution? Can complex systems arise naturally and spontaneously into higher tiers of complexity and order and opportunity—according to the Second Law of Thermodynamics— and all without divine intervention commonly described as Intelligent Design or Irreducible Complexity?

Sean Carroll has much to offer on this question:

Entropy and Complexity, Cause and Effect, Life and Time

Participants should refrain from arc-reflex boiler-plate diatribes echoing previously held opinion and first examine what Carroll has to say. Failure to do so will merit cyber-smack downs.

Why Evolution Matters

Because evolution proves that God does not exist. Except when it doesn’t.

In June 2004, the science historian Frank Sulloway and I began a month-long expedition to retrace Charles Darwin’s footsteps in the Galápagos Islands. It turned out to be one of the most physically grueling experiences of my life…

– Shermer, Michael. Why Darwin Matters: The Case Against Intelligent Design.

Just like taking a pilgrimage. All hail Darwin.

Any other Darwin worshipers here who have taken the Darwin pilgrimage?

What motivated you to try to retrace the footsteps of your master?

Science, not theology, should decide the merits of Intelligent Design

Over at Biologos, an evangelical theologian named Robin Parry has written a hit piece titled, God is More Than an Intelligent Designer. Now, I have no problem with someone criticizing Intelligent Design. But I do have a problem when someone criticizes it without getting out of his armchair and taking a look at the evidence for and against it. My own position is that Intelligent Design theory should be evaluated on strictly scientific grounds. Parry, unfortunately, criticizes it for all the wrong reasons, which can be summed up in a single, dismissive phrase: “Your God is too small.”

Is Parry right? Let’s have a look at his arguments.

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A corrected worksheet targeted for High School students proving that even if Photosynthesis were IC – it would still be evolvable.

This is my second kick at the can and a follow up to my last OP called:

A worksheet targeted for High School students proving once and for all that Photosynthesis is not “Irreducibly Complex”

In deference to Keiths, I have changed the title.

I want to thank participants for their insightful suggestions… yes that includes you Sal. I even included your frog metaphor.

Special thanks go to Mung and to Bill!

A very deep bow and tip of the hat goes to Keiths.


I would appreciate any feedback and suggestions for improvement before I finalize it and submit to the Biology Teachers’ cyber-community for their perusal.

ENV’s shockingly bad argument that humans are products of intelligent design

If you were going to argue that any species on Earth is the product of intelligent design, then humans would be a pretty logical choice – after all, we’re the only species that’s capable of knowing whether we’re designed, and if so, of inquiring as to who our Designer might be. That makes us a pretty remarkable species. In a recent unsigned post, Evolution News and Views attempts to summarize the evidence for humans as products of intelligent design. Unfortunately, it does such a poor job that it ends up shooting itself in the foot. In this post, I’d like to highlight the questions which any halfway-decent case for humans being design products needs to address, and suggest a few answers.

Briefly, the questions which any theory positing that humans were designed needs to answer are as follows:

(1) What exactly are human beings?
(2) Which physical and mental attributes of human beings can we confidently say were designed?
(3) Did these attributes all appear at once? And if not, what are the implications for human equality?
(4) Which hominins in the fossil record qualify as human?
(5) Can we identify the point in the fossil record at which human beings appear, as products of intelligent design? If not, why not?

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most of the mutations

But not all of them. It’s interesting that even the most hardened creationists who have exposure to some science still cannot quite bring themselves to rule out the possibility of a beneficial mutation. Here’s Sal:

Much (not all) the heterozygosity and alleles were created and thus differences were strategically positioned to not cause functional compromise and most of the mutations thereafter are rare variants and slightly damaging.

So if most are slightly damaging then a few are beneficial. And if a few are beneficial then even fewer will be highly beneficial.

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