John Wilkins Revisits Methodological Naturalism

Thank God John has revived Evolving Thoughts!

As usual, his latest post contains lots of food for thought [God and evolution 2: The problem of creation]. I want to pick out one morsel because it's back in the news recently.

It's the problem of "methodological naturalism" and whether it restricts science. Kairosfocus recently posted an article on methodological naturalism at Uncommon Descent [Optimus, replying to KN on ID as ideology, summarises the case for design in the natural world]. He pointed out, quite correctly, that by restricting science to methodological naturalism it means that Intelligent Design Creationism becomes non-scientific by definition.

I've argued frequently in the recent past that science is not bound by methodological naturalism [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism]. My stance has evolved over the past few years. Back in 2007 I was a staunch defender of limiting science to methodological naturalism [Methodological Naturalism].

Jerry Coyne agrees with my current position on methodolocical naturalism. We are both upset by the way it's used to support accommodationism at NCSE [The NCSE Position on Science vs Religion] and at AAAS [AAAS Supports Accommodationism, Illogically]. If you're new to the subject, read Jerry's latest post at: Must we assume naturalism to do science?. That will bring you up to date.

John Wilkins and I have debated this controversy several time [e.g. John Wilkins Defends Methodological Naturalism]. The important point, as far as I'm concerned, is that there are respectable philosophers who disagree with the idea that science can't investigate the supernatural because it is constrained by methodological naturalism.

Here's what John said yesterday (in my time zone).

The term “naturalism”, however, is ambiguous. On the one hand it can mean giving a natural explanation through the use of scientific methods such as the use of human reasoning and observation. Or, it can mean the claim that only “natural” things exist. The first is sometimes called “methodological naturalism”, and it is the underpinning of all science, and indeed all learning about the world. The second is sometimes called “metaphysical naturalism”, although I think it is instead a claim about what exists (which is called “ontology” amongst the philosophical community). God might be natural in that sense. There is no real sharp dividing line between the natural and the supernatural that would satisfy most believers. For example, human nature for some is held to include a soul, which is divine. So let us call the second kind ontological naturalism.

Obviously I don't think that methodological naturalism is the "underpinning of all science." I think science is free to investigate claims of the paranormal (i.e. not naturalism) and can, in principle, discover things that don't meet the definition of naturalism.

What makes me nervous is that this is John's field. Is he saying that among philosophers of science the overwhelming consensus believes that that in science you can only give natural explanations? Or is he simply offering his personal opinion disguised to look authoritative?

Is there a slam-dunk philosophical refutation of the position held by the likes of Yonatan Fishman and Maarten Boudry that Jerry Coyne and I (and many others) are unaware of?

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Hank Green Talks About Junk DNA

A reader gave me a link to a video that was posted on Genetic Engineering & Biotechnology News (GEN) just a few days ago (March 25, 2013). The video was made by Hank Green of SciShow. Hank has a bachelor's degree in biochemistry and a master's degree in environmental studies.

The video is interesting for two reasons: (1) it shows how a typical scientifically literate person interpreted the ENCODE publications, and (2) it show how a business publication treats the results almost seven months later. Here's how GEN introduces the video ...

GEN brings you the best, most informative and/or entertaining biotech-related videos on the web!

In this video, Hank—who has brought you updates on the Human Genome Project, chimeras, and epigenetics—explains why your junk DNA may actually be quite valuable. Through the ENCODE project, scientists have recently revealed that junk DNA is in fact useful in ways we hadn't understood. Though there's still a lot to learn, Hank explains why it's an exciting time to be studying genes.

Watch the video and tell me what you think.

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Understanding the ENCODE Results

Josh Witten of The Finch and the Pea participated in a video discussion about the ENCODE results [see Decoding ENCODE]. The hosts are Rajini Rao, Buddhini Samarasinghe and Scott Lewis. The other guest is Ian Bosdet. The goal is to explain the controversy over ENCODE in a way that the general public can understand.

Post a comment and let me know what you think. Do you understand the issues after watching the video?

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Responding to 21st Century Atheism

I'm going to a meeting (Responding to 21st Century Atheism) on Saturday, April 13. Are you going?

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Education Is a Two-Way Street

I recently met Melonie Fullick and I've been reading her blog: Speculative Diction. Here's another post that really hits the nail on the head: Can education be sold?. As usual, you have to read the whole post but this is the part that resonates with me ...

Education works in much the same way: it is a process, one in which the student plays a necessary part, and an experience, in which the student plays a major role in the “outcome”. In fact every student actually receives a different “education”, with different outcomes, even if they’re all paying the same amount. What you pay for with tuition money is not “education”, but access to resources–libraries, expert staff, teaching and mentorship, even social contact–and access to a formal credential. Even the credential isn’t guaranteed, since students must complete academic requirements in addition to paying tuition and fees.

The assumption that education itself can be sold seems in part like a conflation of “education” and “credential”, and also an assumption that education never required anything from the student in order to be education. The idea that in the past students were not “engaged” with material is closely related to this. Of course students in the past were engaged to learn–they had to be. Otherwise they couldn’t have learned anything, because that’s how learning works. This is why “education” cannot be “delivered” like the daily paper.

The concept of education as an object is also present in debates about online learning, particularly in the recent massively hyped corporate and Ivy League versions of MOOCs. Driven as they are by the non-pedagogical need to find economies of scale, these projects envision students quantitatively, from the calculation of enrollment to the use of “learning analytics” to track behaviour (and the monetization of data). This fragmentation turns education into a series of discrete services, interactions, and measured outcomes.

Such a view of education–as something that can be delivered, sold, packaged–is part of a schema that includes the overly-simplistic “sender-receiver” model of communication, and the objectification of knowledge. These ideas are present in much of the criticism of, and commentary about, higher education; and they are pervasive in the rhetoric of education marketing and policy. The marketization of education, its presentation as simultaneously a product and a service, its increasing necessity in a difficult economy, and the financial burden placed on students through increasing tuition and fees, have all contributed to our understanding of what education is. Objectification and commodification go hand in hand; treating students as consumers means encouraging them to see education as something to be consumed–not created. Of course this is much easier than saying, “you’ve paid $6,000–now you have to do the work”, because that arrangement simply doesn’t fit with consumerist logic.

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Teach Students How Universities Work

I recently met Melonie Fullick and I've been reading her blog: Speculative Diction. Melonie is a graduate student at York University in Toronto (Canada). Her main interest is universities and how they work.

I highly recommend her blog and I'm going to highlight a few of her posts. The first is Mixed Messages where she talks about what students know about universities and what they should know. Here's how she begins ...

A central part of my research project is the way organizations communicate, and the organizations I focus on are universities. So when it comes to undergraduate education and university experience, an important question I think we need to ask is this: what’s the message that students receive from universities? I’ve been thinking about this lately, and was discussing it again last week with students in one of my tutorials. Here are a few of the thoughts that came out of that discussion.

You should read her entire post but here's the bottom line ...

So what’s the message that students receive from universities? From asking undergraduates, it sounds like oftentimes it’s an incoherent, authoritative, and monologic one. This tone and delivery in and of itself can be off-putting enough that students might feel uncomfortable seeking help. For example, being told “that information was/is available to you” (i.e., “you should have known better”) is not a helpful approach when students may be confused and in the middle of a crisis, seeking support. One thing that’s missing is the understanding that rather than just providing students with lists of available services, we need to de-mystify the university itself; instead of trying to create the perfect bureaucratic system (which is impossible in any case), we could show students how systems work. This is also part of the “tacit” knowledge that students gain from being in university; to help students understand the institution, we need to make that knowledge explicit–to communicate it.

I've often thought that we must not be doing a good job of education if we are graduating students with a bachelor's degree who don't understand the basics of how a university works. These are the students who will go on to decide the future of universities even if it's only because they vote. How do we "de-mystify" the university?

This reminds me of a Forbes article published last January by Susan Adams [The Least Stressful Jobs Of 2013]. You may recall that there was a bit of a kerfluffle about it in the blogosphere (e.g. I Have the Least Stressful Job!!!]. Melonie Fullick also wrote about it in More (higher ed) media madness!. Let me remind you of what Susan Adams said in her article ...

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

In an ideal world, every single university graduate should know that this is ridiculous. They should know what professors really do because they have spent four years at university and they learned how the system works. How is it possible that we are graduating students who would believe something like this?

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Learning About Evo-Devo

We talked about evolutionary developmental biology (evo-devo) in my class last week. The main issue is whether the proponents of evo-devo are making a substantive contribution to evolutionary theory. Is evo-devo going to be part of an extended modern synthesis, and, if so, how? My own view, which I express to the class, is that the discoveries of developmental biology pretty much confirm what Stephen J. Gould wrote in Ontogeny and Phylogeny back in 1977.

What, then, is at the root of our profound separation? King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation: small changes in the timing of development can have manifold effects upon a final product "Small differences in the timing of activation or in the level of activity of a single gene could in principle influence considerably the systems controlling embryonic development. The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts." Differences in regulation may evolve by point mutations of regulatory genes or by rearrangement of gene order caused by such familiar chromosomal events such as inversion, translocation, fusion, and fission. Studies of banding indicate that at least one fusion and ten large inversions and translocations separate chimps and humans.

Stephen J. Gould (1977) Ontogeny and Phylogeny, Harvard University Press, Cambridge Massachusetts, USA pp. 405-406

This helps us understand the history of life, especially the evolution of animals, but it doesn't contribute to evolutionary theory.

PZ Myers is teaching a developmental biology course and his students are dealing with three take-home questions this weekend [What I taught today: O Cruel Taskmaster!]. I'd like to reproduce two of them here since they're very relevant to the debate over the importance of evo-devo.

Question 1: One of the claims of evo devo is that mutations in the regulatory regions of genes are more important in the evolution of form in multicellular organisms than mutations in the coding regions of genes. We’ve discussed examples of both kinds of mutations, but that’s a quantitative claim that won’t be settled by dueling anecdotes. Pretend you’ve been given a huge budget by NSF to test the idea, and design an evodevo research program that would resolve the issue for some specific set of species.

I'd like my students to keep in mind Richard Lenski's ongoing evolution experiment in E. coli. Recall that evolution of the ability to grow on citrate depended mostly on mutations that changed the regulation of citrate utilization genes.

Since we have many examples of mutations that affect regulation of gene expression in bacteria, yeast, and other single-cell organisms, why do the proponents of evo-devo think they're on to something special when they look at development in animals? What is there about the evolution of "form" that changes our views on evolution?

Question 2: Every generation seems to describe the role of genes with a metaphor comparing it to some other technology: it’s a factory for making proteins, or it’s a blueprint, or it’s a recipe. Carroll’s book, Endless Forms Most Beautiful, describes the toolbox genes in terms of “genetic circuitry”, “boolean logic”, “switches and logic gates” — he’s clearly using modern computer technology as his metaphor of choice. Summarize how the genome works using this metaphor, as he does. However, also be aware that it is a metaphor, and no metaphor is perfect: tell me how it might mislead us, too.

Before answering PZ's question about Sean Carroll and metaphors, I'd like my students to remember the quotation I gave them in class. Discuss the use of hyperbole and metaphor in this context.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

This book tells the story of this new revolution and its insights into how the animal kingdom has evolved. My goal is to reveal a vivid picture of the process of making animals and how various kinds of changes in that process have molded the different kinds of animals we know today and those from the fossil record.

Sean B. Carroll Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton & Co., New York (2005) p. x

I'd also like Sandwalk readers to keep in mind the recent ENCODE publications. They talked extensively about genetic circuits and regulation. In fact, their major "finding" was the idea that our genome is full of regulatory elements; so many, in fact, that most of what we thought was junk DNA is actually part of a a vast control circuit. Has this emphasis on a multitude of switches and controls been misleading or is it turning out to be correct?

I would ask a third question. The evolution of toolkit genes (i.e. transcription factors) make it possible to evolve many different body plans with only a small number of mutations. It helps explain the Cambrian explosion. Given our current understanding of evolution, is it possible to select for a evolution of a toolkit that has this potential for future evolution? Explain your answer.

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ENCODE, Junk DNA, and Intelligent Design Creationism

andyjones has replied to my earlier posting on ENCODE and junk DNA. You can read his response at: (More) Function, the evolution-free gospel of ENCODE. Here's part of what he says ...

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither.

It's true that there are some IDiots who are distancing themselves from a commitment to junk DNA. There are probably some who claim that they could live with the fact that 90% of our DNA is junk.

But let's not forget that Jonathan Wells is a prominent IDiot and he wrote a book on The Myth of Junk DNA. It sounded very much like Intelligent Design Creationism is staking its reputation on finding function for most of our genome.

The Hardy-Weinberg Equilibrium

It's important to understand modern evolutionary theory and that means it's important to understand the Hardy-Weinberg Equation and what it means.

The significance is explained in all the leading textbooks on genetics and evolution. I've chosen the explanation given by Carl Zimmer and Douglas Emlen because I know that Carl has spent a good deal of time getting it right in his new book Evolution: Making Sense of Life.

Imagine that you have a population with two alleles, A and a, at a single locus. The frequency of the first allele is f(A) to which we assign the value p. The frequency of the second allele is f(a)=q. In a randomly mating sexual population the probability of an A sperm being produced is p and the probability of an a sperm being produced is q. Similarly, the probability of an A egg cell is p and the probability of an a egg cell is q. These probabilities, p and q, do not have to be equal.

We can calculate the probabilities of all possible combinations or sperm and eggs in the population from a the following diagram (Punnett square). This one is from Wikipedia.


Since the total probability has to equal one, we have ....

p² + 2pq + q² = 1

This is the Hardy-Weinberg equation or the Hardy-Weinberg Equilbrium. What does it mean? Let's quote Zimmer and Emlen (page 156).

Hardy and Weinberg demonstrated that in the absence of outside forces (which we describe later), the allele frequencies of the population will not change from one generation to the next. As we'll see below, this theorem is a powerful tool for population geneticists looking for evidence of evolution in populations. But it's important to bear in mind that it rests upon some assumptions.

One assumption of the model is that a population is infinitely large. If a population is finite, allele frequencies can drift randomly from generation to generation simply due to chance variation, in which alleles happen to be passed on to the next generation. (We will explore genetic draft in detail later in the chapter.) While no real population is infinite, of course, very large ones behave quite similarly to the model. That's because variation due to chance is inconsequential, and the allele frequencies will not change very much from generation to generation.

The Hardy-Weinberg theorem also requires all of the genotypes of the locusts are equally likely to survive and reproduce. If individuals with certain genotypes produced twice as many offspring as individuals with other genotypes, for example, then the alleles that these certain individuals carry will comprise a greater proportion of the total in the offspring generation than would be expected given the Hardy-Weinberg theorem. In other words, selection for or against particular genotypes may cause the relative frequencies of alleles to change and results in evolution.

Yet another assumption of the Hardy-Weinberg theorem is that no alleles enter or leave a population through migration. This assumption can be violated in a population if some individuals disperse out of it or if new individuals arrive. The model also assumes that there is no mutation in the population, because it would lead to new alleles

In each of these four cases, the offspring genotype frequencies will differ from the equilibrium predictions of the Hardy-Weinberg theorem. That is, because they alter allele frequencies from one generation to the next, selection, migration, and mutation are all possible mechanisms of evolution.

The Hardy-Weinberg theorem is useful because it provides mathematical proof that evolution will not occur in the absence of selection, drift, migration, or mutation. By explicitly delineating the conditions under which allele frequencies do not change, the theorem serves as a useful null model for studying ways of allele frequencies do change. The Hardy-Weinberg theorem helps us understand explicitly how and why populations evolve. By studying how populations deviate from the Hardy-Weinberg equilibrium, we can learn about the mechanisms of evolution.

There you have it. The Hardy-Weinberg describes the situation where evolution DOES NOT HAPPEN and thus serves as the null hypothesis for testing whether evolution is happening. Every undergraduate knows this.

Let's see if the Intelligent Design Creationists know this. I'm quoting "niwrad" from a post on one of the leading ID websites, Uncommon Descent: The equations of evolution.

For the Darwinists “evolution” by natural selection is what created all the species. Since they are used to say that evolution is well scientifically established as gravity, and given that Newton’s mechanics and Einstein’s relativity theory, which deal with gravitation, are plenty of mathematical equations whose calculations pretty well match with the data, one could wonder how many equations there are in evolutionary theory, and how well they compute the biological data related to the Darwinian creation.

....

The Hardy-Weinberg law mathematically describes how a population is in equilibrium both for the frequency of alleles and for the frequency of genotypes. Indeed because this law is a fundamental principle of genetic equilibrium, it doesn’t support Darwinism, which means exactly the contrary, the breaking of equilibrium toward the increase of organization and creation of entirely new organisms. To claim that the Hardy-Weinberg law explains evolution is as to say that in mechanics a principle of statics (immobility) explains dynamics (movement and the forces causing it).

....

So the initial question, how well math support Darwinian evolution, has the short answer: it doesn’t support evolution at all. Despite of the pretension of evolution to be a scientific theory with the mathematical certitude of the hard sciences, properly the equations of evolution do not exist.

As you can see, the Intelligent Design Creationists interpret the "Hardy-Weinberg law" very differently, I wonder who is right?

Let's check with Joe Felsenstein. He's an expert on population genetics so he should know. Read his decision at: Evolution disproven — by Hardy and Weinberg?.

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He Likes Me ... He Really Likes Me!

David Klinghoffer likes me and he's not afraid to say so [Laurence A. Moran, University of Toronto Biochemist and Darwin Skeptic]. He says,

Welcome aboard, Dr. Moran! The U. of Toronto biochemist surprised us by indicating in a post at his Sandwalk blog that he could sign on to the statement in the Scientific Dissent from Darwinism ....

Let me remind readers what the statement says ...

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

Just about every evolutionary biologist would have to agree with this statement if they were being honest. So why is this such a big deal for the Intelligent Design Creationists? Why do they promote their list of signatories in their publications and why do they continue to solicit signatures on their website? [A Scientific Dissent from Darwinism]

David Klinghoffer has the answer. Do you believe him?

... no one says that the signers of the Dissent list are creationists, other than Darwin advocates who dishonestly try to cement the absurd, fallacious equation of Darwin skepticism with Young Earth Creationism. The list has nothing to do with creationism. Nor does it say anything about intelligent design, which also has nothing to do with creationism.

Okay, so the list has nothing to say about intelligent design. So what is its real purpose?

Any scientist who agrees with the statement that heads the Scientific Dissent from Darwinism is a Darwin doubter, that's all -- and congratulations to him or her! Simply to relay the fact of his skepticism on orthodox evolutionary theory is hardly a misuse of anyone's name. It just reports some interesting and good news. What's wrong with that? For Darwin defenders, the thing that's wrong is that it undercuts their main defense: the assertion that nobody doubts Darwin's theory, or only religious nuts do so, and so there is no legitimate controversy on evolution.

We've always said that private doubts about Darwinian theory are far more widespread in scientific life than the media let on. Now on that point we have Dr. Moran's helpful confirmation.

Hmmm ... that's what this is all about? The IDiots know full well that most evolutionary biologists aren't strict Darwinists but they just want this to become more widely known? If that's true then they could certainly help out by explaining the correct version of modern evolutionary theory—including random genetic drift— to their supporters and advising them not to use the term "Darwinism" as a synonym for "evolution." That would make sense, right?

From now on, I expect David Klinghoffer and all his friends to use "modern evolutionary theory" to describe the position of their opponents. I expect them to avoid the word "Darwinism" since, by their own admission, they know that it's wrong.

Not holding my breath .....

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The title of this post is a reference to a statement by Sally Field

at her Oscar acceptance speech in 1985. I know that I'm paraphrasing a misquote.

Doug Axe Challenges Darwinian Evolution

Here's a video where Douglas Axe tries to explain why Darwinism is wrong. I'm going to let Sandwalk readers discuss the many flaws in his argument but first I want to mention two things.

1. Jeffrey Shallit shows that his statements about information theory are about as accurate as his statements about evolution. [Doug Axe Doesn't Understand Information Theory]
2. Like most IDiots, Doug Axe continues to equate Darwinism and natural selection with evolution. He does this in spite of the fact that his colleague, Ann Gauger, claims to understand the difference. According to her, scientists who doubt Darwinism can still be firm supporters of evolution. If the IDiots actually believe this then why do they keep using the term "Darwinism" to describe their opponents?

The bit about junk DNA in the video reveals that Doug Axe doesn't known dick about evolution or Darwinism. The version of evolution known as Darwinism rejects the idea that most of our genome is junk. I don't think Doug Axe can handle that kind of truth.



Remember folks, this is just about the best they have to offer.

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I'm a New Friend of Ann Gauger

A few days ago I posted a message about the IDiots' list, A Scientific Dissent from Darwinism, of people who disagree with Darwinism. I specifically mentioned Joshua Youngkin who said that, " 'A Scientific Dissent from Darwin,' is a thorn in the side of those who say there's no scientific debate over whether evolution works in a completely naturalistic fashion." [Our "Scientific Dissent from Darwin" List: A Reader Inquires] Let's be clear about what he said, he said that the list reveals scientific debate over whether "evolution works in a completely naturalistic fashion." In other words, people who sign the list must be non-naturalists. That's another word for creationist.

Here's the statement ...

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

Note that the statement says noting about whether evolution works in a completely naturalistic fashion. The IDiots know full well that most scientists would agree with the statement taken at face value but we all know that the IDiots will misuse the statement just as Joshua Youngkin did on the Evolution News & Views blog. You can find further proof of the treachery of the IDiots at the list website where the following quote from someone named Raul Leguizamon is prominently featured on the home page.

I signed the Scientific Dissent From Darwinism statement, because I am absolutely convinced of the lack of true scientific evidence in favour of Darwinian dogma. Nobody in the biological sciences, medicine included, needs Darwinism at all. Darwinism is certainly needed, however, in order to pose as a philosopher, since it is primarily a worldview. And an awful one, as George Bernard Shaw used to say.

The implication is clear.

Ann Gauger is thrilled to discover that I'm not a Darwinist [Our New Friend, Laurence A. Moran]. I guess she's under the impression that if you're not a Darwinist then you must be an IDiot like her.

Here's how her mind works ...

1. People on the Dissent from Darwinism list are supporters of the statement.
2. Larry also agrees with the dissent statement.
3. Larry says only IDiots claim that supporters of this statement are creationists.
4. Larry says that Project Steve is a excellent parody of the "creationist" list, thus in effect calling supporters of the statement creationists.

Wait. Following the logic there, that would seem to make Dr. Moran an IDiot, in his own eyes anyway. Not that, in pointing this out, I mean it unkindly.

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Who Owns Your Genome?

The sequence of your genome contains lots of information about you. It also contains lots of information about your parents, your siblings, and your children. That's why you should not make your genome sequence public without obtaining their permission.

The sequence of Henrietta Lacks' genome was just published (HeLa cells) and nobody bothered to seek permission from her survivors. Jonathan Eisen has a comment and he has also collected all the information on the internet [HeLa genome sequenced w/o obtaining permission/consent from family - some comments and background]. Be sure to read the New York Times article by Rebecca Skloot: The Immortal Life of Henrietta Lacks, the Sequel. She says,

LAST week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours.

In my opinion, there is no excuse for publishing this genome sequence without consent.

Razib Khan disagrees. He thinks that he can publish his genome sequence without obtaining consent from anyone else and I assume he feels the same way about the sequence of the HeLa genome [Henrietta Lacks’ genome, and familial consent].

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Do Invertebrates Really Make Up 80% of All Species on Earth?

bug_girl has a new post called Planet of the Arthropods. She asks why we should care about invertebrates, "Why should we care about a bunch of squishy boneless animals? Because invertebrates make up EIGHTY PERCENT OF ALL THE SPECIES ON EARTH. They truly are the 'little things that run the world.'"

She links to this image ...


Isn't that amazing! Single-celled eukaryotes, fungi, and bacteria make up such a small percentage of total species (<1%) that they don't even register on this summary!

Here's a phylogeny of eukaryotes (no bacteria) from Keeling et al. (2005). If you look closely, you can find "animals" down in the lower right-hand corner. Isn't it amazing that one little insignificant branch represents 83% of all species on the planet? Seriously, something is wrong with taxonomy if this is even close to being true.


Estimates of the total number of bacterial species range from about one million to about one billion [Jonathan Eisen]. Read Carl Zimmer's New York Times article: How Many Species? A Study Says 8.7 Million, but It’s Tricky for an interesting perspective.

The general public has a very poor understanding of our relationship to all other species on this planet. We should be working hard to dispel the major misconceptions about biology and evolution.

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Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676. [doi:10.1016/j.tree.2005.09.005]

Estimating the Human Mutation Rate: Direct Method

This is the fourth in a series of posts on human mutation rates and their implication(s). The first three were ...

What Is a Mutation?
Estimating the Human Mutation Rate: Biochemical Method
Estimating the Human Mutation Rate: Phylogenetic Method

There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method.

The Biochemical Method is based on our knowledge of biochemistry and DNA replication as well as estimates of the number of cell divisions between zygote and egg. It gives a value of 130 mutations per generation. The Phylogenetic Method depends on the fact that most mutations are neutral and that the rate of fixation of alleles is equal to the mutation rate. It also relies on a correct phylogeny. The Phylogenetic Method gives values between 112-160 mutations per generation. These two methods are pretty much in agreement.

The Direct Method involves sequencing the entire genomes of related individuals (e.g. mother, father, child) and simply counting the new mutations in the offspring. You might think that the Direct Method gives a definitive result that doesn't rely on any assumptions, therefore it should yield the most accurate result. The other two methods should be irrelevant.

This would be true if the Direct Method were as easy as it sounds but things are more complicated.