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Showing posts from October, 2009

Antievolution and species fixity

Paul Garner sparked a bit of debate when he posted the simple claim that young earth creationism is not the same as species fixity. Forty comments later, it's still being debated. A responder who goes by the name "WebMonk" basically claims that until only recently, species fixity was the majority creationist position advocated by mainstream creationists. In his words,
Creationist biologists may have rejected species fixity for many decades, but the Creationists MOVEMENT certainly promoted it, and still does quite widely.Unfortunately, much of the follow-up comments have gotten lost in the minutiae, since I think WebMonk is quite right in this basic claim. The wider creationist movement does indeed accept species fixity, and the major creationist organizations have only recently begun trying to fix that problem.

To show you why I think so, I'm first recommending reading over my paper on species variation and creationism [PDF], particularly the part about antievoluti…

Microbes continue: pathogens and genomic islands

The ARJ microbe series continues this week with Georgia Purdom's "The role of genomic islands, mutation, and displacement in the origin of bacterial pathogenicity." Previous entries in the series:

Francis & Purdom: "More abundant than stars: an introductory overview of creaation microbiology"
HTML - PDF - My comments

Liu & Soper: "The natural history of retroviruses: exogenization vs endogenization"
HTML - PDF - My comments

Criswell: "A review of mitoribosome structure and function does not support the serial endosymbiotic theory"
HTML - PDF - My comments

Sherwin: "A possible function of Entamoeba histolytica in the creation model"
HTML - PDF - My comments

Loucks: "Fungi from the biblical perspective: design and purpose in the original creation"
HTML - PDF - My comments


This new paper is a good one. This was the first in the microbe series that made me excited to read it. To be honest, this is the first creationist paper …

Genome evolution & speciation

Regular readers will recall my interest in genome evolution, particularly as it relates to the origin of new species (here and here). Two significant papers on this subject are available this week. In the first, Barrick et al. looked at adaptation in a laboratory population of E. coli evolving over 40,000 generations. They sequenced six genomes of E. coli from generations 2,000, 5,000, 10,000, 15,000, 20,000 and 40,000 as well as the ancestral E. coli genome for that population. They discovered a surprisingly high and constant rate of beneficial mutations, only a fraction of which were single nucleotide substitutions. Remarkably, all 26 point mutations found in coding regions were non-synonymous, which suggests that the changes were not just neutral drift. Fourteen of these genes with mutations were sequenced in eleven other 20K-generation populations derived from the same ancestor. They found that only twelve of the fourteen genes modified in their population were also modifie…

The nature of faith

I've been putting this entry off, mostly because I'm not entirely sure what faith is. I'm quite sure I know what it isn't, though, so let's start there.

Faith is not merely agreement, nor is it an optimistic feeling, nor is it acceptance of something without or against evidence. These are all modern stereotypes of faith that have little to do with real faith.

Faith is also not just an emotion. Faith can certainly be emtional, but it's not just an emotion. There have been plenty of times that my faith has told me to do something I really don't feel like. And it's not just some guilt feeling either: There have been times I knew by faith that I should do something neither good nor bad but something I still didn't want to do. Figure that one out. Besides, if it was easy or emotionally desirable to be a Christian, lots of people would be Christians.

Faith is also not entirely rational. If Christianity were merely a case of weighing evidence and comi…

BSG Newsletter and Conference

The BSG just released its second newsletter at the BSG website. There are short items by Roger Sanders and Joe Francis, and a blog entry from yours truly. BSG members can download the newsletter from the BSG website. Just log in and click on "newsletter." Thanks to Jonathan Bartlett for handling all the editorial duties for the newsletter.

Also, don't forget the coming conference at Truett-McConnell College, held jointly with the Creation Geology Society. The past couple years we've been at conference centers, which unfortunately increased our cost substantially. By moving back to college-hosted conferences, we're hoping to lower the cost and attract more people. Once again, the conference will be the last weekend in July. Abstracts will be due at the end of March, so be thinking about research projects now. I'll have more details on abstract submission as the day approaches.

Microbes continue: entamoebas and fungi

First, a correction on my previous entry. I mentioned the idea that bacteria might be considered external organelles. I knew that I'd heard the idea from Joe Francis, but I couldn't remember the precise citation. I cited his Answers Magazine article, but it was actually in the Microbe Forum proceedings from 2007. Now, on with the show.

Here's a recap on previous papers in the ARJ microbe series:

Francis & Purdom: "More abundant than stars: an introductory overview of creaation microbiology"
HTML - PDF - My comments

Liu & Soper: "The natural history of retroviruses: exogenization vs endogenization"
HTML - PDF - My comments

Criswell: "A review of mitoribosome structure and function does not support the serial endosymbiotic theory"
HTML - PDF - My comments

I'm going to cover two papers in this entry because I don't have a lot to say about them. First is Sherwin's "A possible function of Entamoeba histolytica in the creation …

Mendel is REALLY not enough

Back in 1927, creationist pioneer Byron C. Nelson published a book called "After its Kind", in which he detailed a theory of species origins based on the science of Mendelian genetics. The basic idea is that the isolation of particular genetic alleles in different populations explains the origin of "new" traits. This idea became quite popular in creationism. For example, Will Tinkle (one of the founders of the Creation Research Society) recycled it as the "theory of heterozygous creation" for his book Heredity: A Study in Science and the Bible. Though statements of this theory have gotten more sophisticated over the years, they're still basically nineteenth century genetics.

Modern comparative genetics and genomics continue to show that Mendelian genetics simply does not explain the changes that occur when a new species originates. I've mentioned this before (Mendel is not enough), and I proposed at the 2003 ICC that genomic rearrangements lea…

Microbes continue: endosymbiosis

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Here's a recap on previous papers in the ARJ microbe series:

Francis & Purdom: "More abundant than stars: an introductory overview of creaation microbiology"
HTML - PDF - My comments

Liu & Soper: "The natural history of retroviruses: exogenization vs endogenization"
HTML - PDF - My comments

The third paper in this series is Dan Criswell's "A Review of Mitoribosome Structure and Function Does not Support the Serial Endosymbiotic Theory." What does that mean? Well, there are two basic kinds of cell architecture, prokarytic and eukaryotic. Prokaryotes are basically like a sac of jelly (OK, they're a LOT more complicated than that, but I'm mostly interested in the architecture). Eukaryotes are also sacs of jelly but inside those sacs they have smaller sacs called organelles. These smaller sacs do stuff like our organs do stuff for us. There's an organelle that digests food (like our stomach), and there's an organelle for energ…

Random Bits 3

There's sort of news on Snelling's new book Earth's Catastrophic Past. Barnes & Noble listed it for presale, to be released on October 28. They even give it an ISBN, but I can't find that number listed in anything that Bookfinder searches. Neither ICR nor Master Books (the publisher listed by B&N) are showing the book in their databases. The B&N price is pretty decent ($40.46 for B&N members) for a $60 book, but I can't guarantee that this is the book I've been waiting for. Sure sounds like it though.

Meanwhile, Paul Garner is lamenting the flip side of what I've been talking about here. I've been complaining about creationist misrepresentation of evolution (as discredited, without evidence, just speculation, etc.). Paul attended a lecture by Denis Alexander, where Alexander defined young-age creationism as belief in species fixity. He rightly points out that this is a stereotype that does not accurately reflect the beliefs of cre…

Microbes continue: retroviruses

As mentioned previously, Answers Research Journal is publishing a series on microbes, which started off with Joe Francis and Georgia Purdom's introduction, discussed here. During the past few weeks, they've published three papers, and as far as I know, we'll get another one this week. Since I've been distracted by everything under the sun lately, I haven't bothered to post anything about these papers, but I'll try to rectify that this week. First up is a paper from Liu and Soper that gives an interesting twist to the origin of retroviruses.

Retroviruses are a class of virus that go through an RNA-to-DNA "reverse transcription" during their life cycle. Usually (in our cells and in many other types of viruses), DNA is used to make RNA, not the other way around. Everyone is familiar with at least one retrovirus, HIV. What most people are not familiar with is the fact that we carry around thousands of copies of retroviruses in our genomes. Since the…

Explanation clarifications

One of my readers wrote in with a couple of interesting questions, which reminded me of a few more points that might be useful. I will try to make my comments brief.

You make a first-approximation distinction between high level and low level theories, which I think is helpful. But where would you see Haldane's famous 'rabbit in the Precambrian' fitting into that? Would that really challenge the high level theory of universal common ancestry, which is what I think Haldane was implying, or do you think it would only falsify a certain set of lower level theories, for example the precise place of the Mammalia in the tree of life?I think it would take more than a Precambrian rabbit to discredit the high level model of common ancestry. High level models do not depend directly on any particular observation, and they usually require more than just one or two contradictions (no matter how spectacular) to discredit them. I suspect that a true Precambrian rabbit fossil would call f…

Random bits for Friday

While Steve Matheson and I were blogging about Notch, someone was doing actual research on the subject! Gazave et al. have an article on the subject in BMC Evolutionary Biology. It's worth a read, especially for those keen on irreducible complexity (hint: it's reducible).

Paul Garner went to the new Darwin exhibition at the Sedgwick Museum at Cambridge, and he has a write-up on his blog. I will try to make time to see it when I'm there next year (hint, hint, Paul).

Kurt Wise's testimony is available for free at the Truett-McConnell website. If you've never heard it, it's worth checking out.

There's a big crater in the ocean floor off the coast of India, and it's much bigger than the Chicxulub crater in the Yucatan. That impact must have been something to see.

The Nature of Explanation

Before I get started on hierarchical explanations, here's a list of the previous substantive posts in this series:

The Truth about Evolution
The Nature of Science
The Nature of Evidence

Today, I want to look more carefully at the way scientists think about their own theories and arguments. Remember what you learned in school about the scientific method? How we start out making observations, from which we formulate hypotheses? Then hypotheses that are tested successfully become theories, and theories that go through rigorous testing become laws. Right. So that's pretty much bogus. I don't know anyone who really follows that pathway in doing science. Instead, what I find is that observations are interpreted within some kind of theoretical framework, a higher level model that informs the interpretation of data. The interaction of high level models and data lead to the formulation of theories or hypotheses that make sense of both. High level models can be held for any num…

Technorati hilarity

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From the file of the weird: Back when I started this blog, I joined a few blog networks to increase my exposure. As far as I can tell, it's done very little to attract viewers, but I did find Technorati useful for tracking blog reactions. They recently changed a lot of their features, and here's what I found today on my blog listing:



See that little button that says "Top 100 Science?" Well, that's new. So I looked up their science blog listing (currently consisting of 1105 blogs), and what did I find? I'm currently number 22:



Notice who's number 25. Apparently, I outrank ID-centric Uncommon Descent. As I browsed the list, I noticed the absence of PZ Myers's infamous science (and anticreationist) blog Pharyngula. Surely I don't outrank him? So I looked up his Technorati listing:



According to Technorati, atheist scientist PZ Myers has a "Top 100 Religion" blog, and I, arch-creationist, have a "Top 100 Science" blog! The ir…

I'm not alone

Feedback on my apparent heterodoxy continues. John Lynch linked to my post on science (where you'll find some lovely comments), and I am quite aware that Cornelius Hunter posted what appears to be some kind of rebuttal on his blog. Thanks to those who emailed me about it.

My doctrinal outburst might have seemed a little overly despairing and even a little redundant (here and here). I don't want anyone to think I'm feeling abused or depressed by this. I knew what I was doing when I posted the truth about evolution, and I'm not the least surprised by the fuss it's created. It's been kind of amusing, really.

Besides all the silly reactions, there have also been some encouraging notes that I wanted to share (with permission of the authors). These all came to me by private email, and I'll maintain the author's privacy by not divulging their identities. I think these reveal something very important: Not all creationists ride the antievolution bandwagon. …

Speaking tour in England

My friends at Biblical Creation Ministries in the UK have invited me back to speak in March of next year. Here's their press release:
BCM to host speaking tour by leading creation biologist

We are delighted to announce that leading creationist researcher Dr Todd Wood will be visiting the UK again next year. He will be arriving on or around 10 March and staying until 17 or 18 March. We hope that a number of our friends and supporters will be willing to set up meetings at which he can speak during his visit.

His itinerary will be coordinated on BCM's behalf by Stephen and Joan Bazlinton. We are grateful to Stephen and Joan for their help in this regard. If you would like to invite Dr Wood to speak at your church or other meeting, please contact Stephen and Joan by email at s.j.bazlinton@googlemail.com.

Dr Wood will be offering a couple of talks. One will consider the nature of science and what it means to be both a creationist and a scientist. The other will provide an informative …

The Nature of Evidence

For those of you trying to keep track of my flow of thought, here's a recap: I opened a can of worms back in September when I casually announced that there was evidence for evolution. That was followed by a lot of responses, many of which surprised me by their content. I followed up my initial post by explaining my own view of science, which I think is quite reasonable and reflects what scientists actually do. Looking at the responses to that, I felt it was necessary to clarify my doctrinal stance.

Originally for this post I wanted to explain how hierarchies of explanation work, but I thought it would be useful to expound on the nature of evidence first. In my last post, I defined evidence as simply data that corresponds to or is consistent with a theory. I come to this definition from my background in biochemistry and from my ongoing readings in the history of science.

In biochem, we deal with submicroscopic phenomena, atoms, and energy, and the like. It's not as if we c…

Neanderthals and Genome Packing

There are some interesting items in last week's issue of Science. First, Michael Balter has a report on the "Human Evolution 150 Years after Darwin" conference held in Gibraltar last month. It reminds me how much we need some serious paleoanthropology in creationism.

The other report I found interesting addresses the question: How do you pack around 40 inches of linear, human DNA into a microscopic nucleus? Lieberman-Aiden et al. use a clever technique to map long-range physical proximity between regions of chromosomes in the human genome. They found that "the chromatinconformation is consistent with a fractal globule, a knot-free,polymer conformation that enables maximally dense packing whilepreserving the ability to easily fold and unfold any genomiclocus." Very elegant.

Balter. 2009. New Work May Complicate History Of Neandertals and H. sapiens. Science326:224-225.
Lieberman-Aiden et al. 2009. Comprehensive Mapping of Long-Range Interactions Reveals Fol…

Darwin's Darkest Hour

Bottom line: I enjoyed it.

Nova's two-hour dramatic special on Charles Darwin starring Henry Ian Cusick wasn't that bad. OK, so the look of the film wasn't precisely correct (that was obviously not Down House, and Darwin was bald by the time he started work on Origin), but the film was generally pretty accurate, not too melodramatic, and filled with delightful little bits from the life of Darwin that it was hard to resist liking it.

The basic storyline follows Darwin in 1858 as he's working on his "big book" to be called Natural Selection. A letter from Alfred Russel Wallace arrives, describing a theory of speciation by natural selection that according to Darwin is nearly identical to his own. In despair, he confides the story of the development of his theory to his wife Emma, which leads to lots of flashbacks of adventures on the Beagle, meetings with such luminaries as Charles Lyell, Joseph Dalton Hooker, and John Gould, and experiments around Down House. …

Basic Types are coming

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One of the projects that we've been working on since I got to CORE is the translation of the German book Typen des Lebens, (Basic Types of Life). The book was originally published in the early 1990s, and we started our translation back in 2000. Nine years later, I'm both relieved and excited to announce that the translation is almost complete. Not only has it been translated, but the articles have been updated, and new articles have been added. Basic Types of Life introduces the concept of basic type biology, in which basic types of species are defined by hybridization (see my Ardipithecus post for more on BT biology).

This coming week, I'll be reading through the latest proof copy of the book, which should be one of the last complete read-throughs. I expect that it will be available for sale in the CORE Issuesseries sometime in the new year (hopefully January). I'll post again when we're closer to the finished product.

I'M A CREATIONIST!

The furor continues, as silly as it is. My blog hits yesterday shot up to heights I've not seen since Pharyngula made fun of me back in March. I've begun to notice a strange undercurrent of folks proposing that I'm not really a young earth creationist. One especially amusing person suggested that I was stupid, possibly bipolar, or just a liar (scroll down here to Lester10's post). So much for that whole "love your enemies" thing.

Lest my creationist credentials be doubted, let me be blunt:

I believe that God created everything that you see in six consecutive days around 6000 years ago.
I believe that Adam and Eve were the very first humans and were directly created by God.
I believe Adam and Eve sinned, and that sin brought death, carnivory, disease, and suffering into the world.
I believe that people really lived to be 900+ years back then.
I believe that there was a truly global Flood that inundated the entire planet.
I believe that humans and land animals wer…

October Genome Research

I love the smell of a new issue of Genome Research. Maybe I'm weird. In any case, there's lots of interesting stuff in this new one. There are a couple of articles on comparative fungal genomics from The Genolevures Consortium and Sharpton et al. There's a really interesting article on comparative genomics in magnetotactic bacteria by Nakazawa et al. They conclude,
Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution.
No surprise there.

The real doozy in this issue is the article by Knowles and McLysaght "Recent de novo origin of human protein-coding genes." They compared human and primate genomes looking for genes in the human genome that are absent in the primates. They filtered out genes that might have been deleted from primates, and they found three genes that had sequences pre…

The nature of science

As I wrote on Saturday, my post about evolution aroused quite a response. Here's a list of the blog reactions that I've found so far:

A Simple Prop
Freedom Log
The GeoChristian
You Call This Culture?
Exploring Our Matrix
for the Sake of Truth
The Clever Badger

(That last one is interesting: I've been badgered by quotes before, but never quoted by a badger.)

John Lynch's post at A Simple Prop started the whole chain reaction. Otherwise, I'm sure my comments would have been ignored like nearly everything else I post. So thanks, John. I guess.

As I wrote before, I expected certain classes of response: (1) Affirmation by anticreationists trying to make other creationists look bad, (2) Denial by antievolutionists convinced that I'm ignorant, brainwashed, or just evil, and (3) intelligent interaction by those who truly understood what I said. I got several responses in each of these categories. I found it very interesting that emails in category (3) tended to open with …

Ardipithecus redux

By now, you've probably already heard about the collection of papers on Ardipithecus ramidus published in Science. Ardipithecus is a fossil hominid, with skeletal features that indicate that it could walk upright or climb trees. Ardipithecus is dated to about 4.4 million radiometric years ago, and the authors of the Science articles interpret as the ancestor of Australopithecus, which in turn were the ancestors of our genus, Homo. Ardipithecus is considered to be somewhat close to the last common ancestor of humans and chimpanzees (which is supposed to have lived a couple million years earlier).

It's kind of strange that all these papers are being published now, fifteen years after the initial fossils were announced in Nature (see White et al. 1994). Usually, the follow-up studies are published in specialized journals, rather than more generalized journals like Science and Nature. Even more unusual is that each of the technical articles is accompanied by a brief, nontechni…