Showing posts from February, 2010

Let's review

OK, people, pay attention. This is important. I seemed to have stirred up a hornet's nest again with my latest post (not quite sure why), and now I'm getting weird reactions/emails again. So let's review:

I'm not an evolutionist!
Frank Marsh wasn't an evolutionist either!
And it doesn't matter what Mastropaolo thinks about me!

Have we got it now? I don't need converting to creationism, thank you. I'm already a creationist. I'm just flabbergasted that with all the blatantly creationist material on this blog, I still get people trying to save my soul.

If I've ruffled your feathers, would it be too much trouble to ask you to at least look at some of the links I list at right, or perhaps google me or look me up on CELDBEFORE you spend your precious time trying to change my mind about evolution? Please?

This is getting old.

Is design an inference?

Steve Matheson is blogging his way through Meyer's new book Signature in the Cell chapter by chapter, and in his most recent post, he asked for my opinion on chapter 7. So here are my thoughts on a single chapter of Signature in the Cell. This is not a review or a critique but rather an expansion of what Meyer wrote. Think of it as "The Rest of the Story."

To start with, I want to say that I generally agree with Meyer about the origin of life (OOL) problem. Given what I know of the issue (and as a biochemist, I think I can give an informed opinion), a naturalistic OOL seems quite intractable. I think there are certain issues (e.g., homochirality, phospholipid bilayer assembly) that are insurmountable without outside "help." From what he's written, I think Matheson would say something like, "Hey, science has figured out so much in the past using naturalistic explanations, why just give up on OOL?" (Perhaps that's an oversimplification and…

Random bits #7

Here's a few things I found interesting (and weird) over the past few days:

First is this paper from the journal Theoretical Biology and Medical Modelling:

Whitacre. 2010. Degeneracy: a link between evolvability, robustness and complexity in biological systems. Theoretical Biology and Medical Modelling 7:6.

From the abstract:
This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms.That makes a lot of sense. I've often thought that the redundancy of genomes might serve some kind of error tolerance function, but if redundancy were also a means of adaptation, that would be a double benefit.

Phil Senter has a really neat article in the February issue of The American Biology Teacher (with a free PDF):

Senter. 2010. Were Australopith…

Is design arbitrary?

I thought I'd start a series on design. Why not? Everyone else is talking about it. Unlike other blogs, though, I'm addressing this one explicitly to Christians. I'll kick off the series with this comment from a reader:
In a sense, common claims by creationists, like "See, it's designed," are arbitrary, but it also seems that we have within us an ability to recognize that these designs came from the Creator "clearly seen."He's responding to a comment I left at Steve Matheson's blog:
The design argument as articulated by Paley was a nearly arbitrary mapping of some of God's attributes (often wisdom and benevolence) to attributes of nature.There are several related issues here. First (related to my point), is there any mapping of divine attributes to features of creation? Second, is the attribution of design to amazingly complex things just arbitrary? Third, aren't we supposed to be able to see God's attributes in creation, as…

The Joys of Editing

There's an interesting editorial in last week's Nature about their editorial practices and choices:

Editorial. 2010. Nature's choices. Nature 463:850.

The editors try to explain some of the editorial processes and dispel some of the negative rumors about how they select papers to publish. As one who has dabbled in editing from time to time, I confess that I enjoyed seeing them squirm a bit.

The truth is that editing is not always fun. Well, it isn't fun if you take it seriously. I've written about the editorial process and peer review on numerous occasions, trying to explain the importance of editing and the need for humility on all sides. I still get criticized for my editorial practices and standards, mostly I think because people are not accustomed to taking correction with grace. It's too bad that human pride so often gets in the way of good writing and editing, but I suppose it's inevitable. If no one was ever offended by an editor's choices,…

Warm oceans and ice ages

There was a new paper of note in ARJ yesterday:

Vardiman, L. and W. Brewer. 2010. Numerical Simulation of Precipitation in Yosemite National Park with a Warm Ocean: A Pineapple Express Case Study. ARJ 3:23-36.

I'm no physicist or climatologist, but I think I can summarize the basic idea. Given a tectonically active global Flood, the oceans would have been considerably warmer immediately after the Flood than they are now. That warmth led to increased evaporation, which led to increased storms. That would lead to snow buildup and glaciation in the higher altitudes and latitudes, thus what folks refer to as an "ice age."

In this new study, Vardiman and Brewer have simulated a higher sea surface temperature in the Pacific Ocean and the resulting increased precipitation in Yosemite and the Sierra Nevadas. Not surprisingly the authors conclude,
Warm sea-surface temperatures increased the precipitation above normal by as much as a factor of four. Based on the likely increase…

Search the Scriptures

After my post on the rete and dogma-driven science, a reader wrote,
... when you say you are "reexamining your interpretations" of Genesis, what do you mean? You can't mean that you are looking at Genesis chapter 1? I thought as young earthers you believe "God said it, I believe it, that settles it"!Yes, when God speaks, that most assuredly settles it, but I am not so naive or arrogant to assert that I always have a perfect understanding of what God said. I believe it's crucially important to constantly evaluate assumptions, which is why I do not accept the "strategy" of hiding creationist assumptions or beliefs under the pretense of doing science. Assumptions need to come out in the open where they can be scrutinized, and those that are wrong must be discarded. For example, my position on min (according to its "kind" in Genesis 1) has changed significantly over the years. So my willingness to examine everything does - and must - ap…

Position open at Truett-McConnell

Are you a young age creationist? Got a Ph.D. in molecular biology, microbiology, or molecular genetics? Looking for a job?
Truett-McConnell College announces a faculty appointment in biology beginning July 1, 2010. The position is full-time and carries faculty responsibilities for teaching basic biology courses at both lower and upper levels, along with assumption of other duties commensurate with full-time faculty status. The position carries full fringe benefits of College employment.Read more in this PDF announcement. Feel free to spread the word.

The little organ that wasn't

I visited the Leonardo Da Vinci exhibit at the High Museum of Art in Atlanta on Saturday. Not being much of an artist myself, I was nevertheless intrigued to see one of his anatomical sketches on display. The sketch was dated to approximately 1492 and depicted sections of the human head. Da Vinci's notes mentioned the rete mirable, the "marvelous network" underlying the brain.

The rete mirable looks like a little sack of worms. It's a complicated net of arteries blood that occurs at the entry of the arteries into the brain. According to Galenic medicine, the rete converted the "vital spirit" of the blood into "animal spirit." Animal spirit was a vaporous stuff that the brain used to send signals to the rest of the body.

There's only one problem with the rete: It isn't really there. The first to notice its absence was Mondino in the early 14th century. In the 16th century, Vesalius, the famous reformer of anatomy and corrector of Gale…

Dmanisi 404

I'm working on a paper on fossil hominids (finally), and I checked out the Dmanisi fossil website here:
Dmanisi: Cradle of the First Europeans

Now I don't mean to pick on them, since they probably get enough crap from insurgents and invasive Russians, but... If you go to that website and click on "Dmanisi Findings," it's 404: "Not Found." I also tried clicking on "Links," which was also 404. Get it? The links are missing.

What can I say? Simple minds, simple humor.

Dinosaur tracks in China

Everyone else is pointing this out, so why not me too? There's a report from the BBC on a fossil find in China: 3000 dinosaur footprints in a 0.64 acre plot. That's one footprint about every 9 square feet, or one every square meter. That's a lot of footprints. Better still: they're all facing the same direction. "Experts" tell the BBC that the footprints "could represent a migration or a panicked attempt to escape predators." Or as Paul Garner said, "other possibilities might suggest themselves from a flood geology perspective." I never tire of the English gift for understatement.

Primordial soup fallout

It's been interesting watching the reaction to the "primordial soup" paper I mentioned last week. Nick Lane (one of the paper's authors) appeared on NPR's All Things Considered. Nothing terribly new there. Same stuff as in the press release. There were some quite predictable blog reactions (at UD and Darwin's God), but the one at PT spawned more than 260 comments. They start out decrying the overhyped press release, then they seem to get derailed debating a couple ID supporters. No surprises there, either.

Then there was this opinion column in the Ottawa Citizen:
Back to the Beginning

That one really made me laugh. The author, David Warren, spends most of the column describing a typical antievolution version of the history of evolutionary theory: Darwin was a story-teller, evolution isn't science, it's atheistic, etc. etc. When he finally gets to the BioEssays paper that inspired his diatribe, he's got only a few hundred words left, and his d…

Aegilops TEs in Mobile DNA

There's a new open access journal called Mobile DNA, which I'll definitely keep my eye on, as I'm a big fan of mobile DNA. From the website:
Mobile DNA is an online, peer-reviewed open access journal that publishes articles providing novel insights into DNA rearrangements, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution.The latest ... issue(?) has a really cool article by Belyayev et al. on transposable elements in wheat relative Aegilops speltoides. They looked at a wild population that
is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites.Their ultimate goal is to try to match these genomic variations to phenotypic changes. This paper doesn't do that quite yet, but it…

Democracy doesn't work?

I heard a really interesting piece on NPR's On the Media today. It's a conversation between the host Bob Garfield the Richard Horton, editor of the British journal The Lancet. They discussed the retraction of a 1998 paper that linked autism to MMR vaccines, in particular how the media hyped the story way beyond the limits, nuances, and refutations of the original research. Here's the audio version:

A Shot of Reality

And here's my transcription of the bit that really caught my attention:
Horton: We don't seem able to have a rational conversation in the public space about difficult, controversial issues without people drawing a conclusion which could be very, very adverse.

Garfield: But is this a case where these conversations would have been better confined to the medical community, that somehow the public should not be participating in these things because we simply don't have the wherewithal to evaluate them?

Horton: I think that although that's a nice thoug…

How to REALLY read Darwin

Over the years I've studied Darwin's Origin and people's interpretations of it, and I've come to a fascinating conclusion. Darwin's work is often misinterpreted. I know, it's not a shocking secret, but there is one persistent and pernicious misreading of Darwin that really gets my goat. I've been procrastinating on writing this, but a comment I left over at Steve Matheson's blog got my thoughts going. So here we go.

Darwin frequently discusses the "theory of creation" in Origin, often contrasting it to his own ideas of descent with modification. I think it's very easy for those of us who hold to a "theory of creation" (there are many) to react negatively to Darwin's constant chiding that creation offers no explanation for a host of facts. In doing so, I think we risk losing track of Darwin's point. In other words, I think it's important to swallow our pride for a moment and actually listen to what Darwin is sayi…

Overselling the origin of life

It's interesting that Nobel prizes in science are often awarded for research that is at least a decade old. The reason is obvious: time gives us perspective; it helps us to discern what research has really made an important impact on science. That advantage of time is apparently lost on many reporters, who frequently oversell the latest research papers that have just been published. Long time readers know of my distaste for the sad state of science journalism and self-promotion (Ida anyone?). So you can imagine my reaction when I read this at ScienceDaily:
For 80 years it has been accepted that early life began in a 'primordial soup' of organic molecules before evolving out of the oceans millions of years later. Today the 'soup' theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth's chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.Pure hilarity. A brand new paper has "ove…