Added April 13, 2006:

Added March 18, 2006:

Added February 17, 2006:

Added February 17, 2006:

This article covers the evidence which leads cosmologists to believe the Big Bang happened, deals with common objections to the theory, and discusses alternative models and questions that still remain to be answered.

Added January 24, 2006:

Added January 10, 2006: A classic and often-referenced 1984 paper by G. Brent Dalrymple. The paper contains short but accurate expositions of radiometric dating methods and discussions of creationist criticisms and attempts to date the Earth as young. It includes material difficult to find elsewhere, such as the discussion of mixing isochrons and the effect of neutron-capture reactions. Dr. Dalrymple is a member of the National Academy of Sciences, a winner of the National Medal of Science, a former president of the American Geophysical Union, and the author of The Age of the Earth

Gwen Pearson, an entomologist formerly known as Bug Girl, has performed sort of a retrospective analysis of the Ark Park‘s facilities for caring for its animals. You might have thought that the Ham-merheaded proprietors of the Ark Park would have performed a prospective analysis but evidently you would have been mistaken. Cheer up! Here is Dr. Pearson’s advice to the Ham-itic designers:... Matt Young http://www.mines.edu/~mmyoung

Razib Khan poked me on twitter yesterday on the topic of David Dobbs’ controversial article, which I’ve already discussed (I liked it). I’m in the minority here; Jerry Coyne has two rebuttals, and Richard Dawkins himself has replied. There has also been a lot of pushback in the comments here. I think they all miss the mark, and represent an attempt to shoehorn everything into an established, successful research program, without acknowledging any of the inadequacies of genetic reductionism.

Before I continue, let’s get one thing clear: I am saying that understanding genes is fundamental, important, and productive, but it is not sufficient to explain evolution, development, or cell biology.

But what the hell do we mean by a “gene”? Sure, it’s a transcribed sequence in the genome that produces a functional product; it’s activity is dependent to a significant degree on the sequence of nucleotides within it, and we can identify similar genes in multiple lineages, and analyze variations both as a measure of evolutionary history and often, adaptive function. This is great stuff that keeps science careers humming just figuring it out at that level. Again, I’m not dissing that level of analysis, nor do I think it is trivial.

However, I look at it as a cell and developmental biologist, and there’s so much more. That gene’s transcriptional state is going to depend on the histones that enfold it and the enzymes that may have modified it; it’s going to depend on its genetic neighborhood and other genes around it; it’s not just sitting there, doing its own thing solo. And you will cry out, but those are just products of other genes, histone genes and methylation enzymes and DNA binding proteins, and their sequences of nucleotides! And I will agree, but there’s nothing “just” about it. Expression of each of those genes is dependent on their histones and methylation state. And further, those properties are contingent on the history and environment of the cell — you can’t describe the state of the first gene by reciting the sequences of all of those other genes.

Furthermore, the state of that gene is dependent on activators and repressors, enhancer and silencer sequences. And once again, I will be told that those are just genetic sequences and we can compile all those patterns, no problem. And I will say again, the sequence is not sufficient: you also need to know the history of all the interlinked bits and pieces. What activators and repressors are present is simply not derivable from the genes alone.

And I can go further and point out that once the gene is transcribed, the RNA may be spliced (sometimes alternatively) and edited, processed thoroughly, and be subject to yet more opportunities for control. I will be told again that those processes are ultimately a product of genes, and I will say in vain…but you don’t account for all the cellular and environmental events with sequence information!

And then that RNA is exported to the cytoplasm, where it encounters other micro RNAs and finds itself in a rich and complex environment, competing with other gene products for translation, while also being turned over by enzymes that are breaking it down.

Yes, it is in an environment full of gene products. You know my objection by now.

And then it is translated into protein at some rate regulated by other factors in the cell (yeah, gene products in many cases), and it is chaperoned and transported and methylated and acetylated and glycosylated and ubiquitinated and phosphorylated, and assembled into protein complexes with all these other gene products, and its behavior will depend on signals and the phosphorylation etc. state of other proteins, and I will freely and happily stipulate that you can trace many of those events back to other genes, and that they respond in interesting ways to changes in the sequences of those genes.

But I will also rudely tell you that we don’t understand the process yet. Knowing the genes is not enough.

It’s as if we’re looking at a single point on a hologram and describing it in detail, and making guesses about its contribution to the whole, but failing to signify the importance of the diffraction patterns at every point in the image to our perception of the whole. And further, we wave off any criticism that demands a more holistic perspective by saying that those other points? They’re just like the point I’m studying. Once I understand this one, we’ll know what’s going on with the others.

That’s the peril of a historically successful, productive research program. We get locked in to a model; there is the appeal of being able to use solid, established protocols to gather lots of publishable data, and to keep on doing it over and over. It’s real information, and useful, but it also propagates the illusion of comprehension. We are not motivated to step away from the busy, churning machine of data gathering and rethink our theories.

We forget that our theories are purely human constructs designed to help us simplify and make sense of a complex universe, and most seriously we fail to see how our theories shape our interpretation of the data…and they shape what data we look for! That’s my objection to the model of evolution in The Selfish Gene: it sure is useful, too useful, and there are looming barriers to our understanding of biology that are going to require another Dawkins to disseminate.

Let me try to explain with a metaphor — always a dangerous thing, but especially dangerous because I’m going to use a computer metaphor, and those things always grip people’s brains a little bit too hard.

In the early days of home computing, we had these boxes where the input to memory was direct: you’d manually step through the addresses, and then there was a set of switches on the front that you’d use to toggle the bits at that location on and off. When a program was running, you’d see the lights blinking on and off as the processor stepped through each instruction. Later, we had other tools: I recall tinkering with antique 8-bit computers by opening them up and clipping voltmeters or an oscilloscope to pins on the memory board and watching bits changing during execution. Then as the tools got better, we had monitors/debuggers we could run that would step-trace and display the contents of memory locations. Or you could pick any memory location and instantly change the value stored there.

That’s where we’re at in biology right now, staring at the blinking lights of the genome. We can look at a location in the genome — a gene — and we can compare how the data stored there changes over developmental or evolutionary time. There’s no mistaking that it is real and interesting information, but it tells us about as much about how the whole organism works and changes as having a readout that displays the number stored at x03A574DC on our iPhone will tell us how iOS works. Maybe it’s useful; maybe there’s a number stored there that tells you something about the time, or the version, or if you set it to zero it causes the phone to reboot, but let’s not pretend that we know much about what the machine is actually doing. We’re looking at it from the wrong perspective to figure that out.

You could, after all, describe the operation of a computer by cataloging the state of all of its memory bits in each clock cycle. You might see patterns. You might infer the presence of interesting and significant bits, and you could even experimentally tweak them and see what happens. Is that the best way to understand how it works? I’d say you’re missing a whole ‘nother conceptual level that would do a better job of explaining it.

Only we lack that theory that would help us understand that level right now. It’s fine to keep step-tracing the genome right now, and maybe that will provide the insight some bright mind will need to come up with a higher order explanation, but let’s not elide the fact that we don’t have it yet. Maybe we should step back and look for it.

Atheist group trying to enhance profile by hosting float in Ellsworth's ...
Bangor Daily News
The float created by an atheist discussion group, the Downeast Humanists and Freethinkers, will feature an evergreen tree, in keeping with the parade's theme “Rock Around the Christmas Tree,” but will emphasize the tree's pagan roots. “We thought it ...

Strange Notions is re-running a fine piece by atheist Tim O'Neill…
Patheos (blog)
on the absolutely ignorant myth of the Dark Ages so beloved by atheists who worship, but almost never use, their intellects. He is that rarest of phenomena, an internet atheist who is knowledgeable, honest and genuinely intelligent, as well as unafraid ...

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NCSE has just announced the second webinar in its ongoing series, to be held on December 18, 2013, at 1:00 p.m. PST. The webinar will focus on “[s]topping bad legislation and encouraging policymakers to support strong science education…,” according to NCSE. The webinar will be led by Josh Rosenau, Programs and Policy Director for NCSE; Vic Hutchison, professor emeritus at the University of Oklahoma, and founder and past president of Oklahomans for Excellence in Science... Matt Young http://www.mines.edu/~mmyoung

O'Reilly Psychoanalyzes Atheists: So Much 'Anger,' 'Are They That Bitter ...
Mediaite
On Friday night, Christmas Crusader-General Bill O'Reilly changed gears to get into therapist mode, attempting to psychoanalyze the motivations of atheists obviously waging a horrible, disgusting War on Christmas™. O'Reilly talked things out with an ...
Atheist Group's Billboard In Times Square: 'Who Needs Christ During Christmas ...Opposing Views
Bill O'Reilly's war on Christmas: Good for atheists' businessWashington Post (blog)
Atheists Want to Abort Christ From Christmas, Says Kooky Alaskan LadyJezebel
Fox News -Western Courier (subscription)
all 17 news articles »

Raw Story
Atheist Ads Banned In Vancouver
Huffington Post Canada
Vancouver's billboards will not play host to an ad promoted by the Centre For Inquiry that endorses an atheist worldview, because the company that owns almost all of the advertising hoardings in the city has refused to run it. The Centre says that ...
Atheist group considers filing human rights complaint after billboard rejectedRaw Story
Atheist Billboard Rejected in CanadaOpposing Views
Atheist billboard ads rejected in VancouverCBC.ca
Christian Post -International Business Times AU -CTV News
all 16 news articles »

Straight.com (blog)
Atheist Ads Banned In Vancouver
Huffington Post Canada
Vancouver's billboards will not play host to an ad promoted by the Centre For Inquiry that endorses an atheist worldview, because the company that owns almost all of the advertising hoardings in the city has refused to run it. The Centre says that ...
The atheist ads Pattison Outdoor doesn't want you to see?Straight.com (blog)
You Won't See This Atheist Billboard in Canada, But Fetus Pics Are OKGawker
Atheist advertising rejected in VancouverVancouver Sun
Lifesite (blog)
all 11 news articles »

How to Share the Gospel With an Atheist
Charisma News
Last week I sat next to James on a flight from St. Louis to Denver. As we talked, the subject turned to spirituality and religion. I confessed that I was a preacher, and he confessed he was an atheist. What unfolded on the rest of the flight was a deep ...
WRIGHT WAY: Are atheists going to 'church?'Cleveland Daily Banner

all 2 news articles »

Film Review: 'The Unbelievers'
Variety
Whatever opinion one has of atheism won't be changed, or even challenged, by “The Unbelievers.” This superficial documentary from first-time feature helmer Gus Holwerda follows scientists and avowed atheists Richard Dawkins and Lawrence Krauss on a ...

Atheist Group Blasts Pryor: 'Theocrats Are Dangerous'
National Review Online
The spot drew criticism from the right, the left, and now, from apolitical atheists. Annie Laurie Gaylor, a spokesperson for the Freedom from Religion Foundation, tells National Review Online that the spot is theocratic and disturbing, and that Pryor's ...

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The Mt. Vernon Board of Education’s attorneys have filed a memo in opposition to John Freshwater’s motion to the Ohio Supreme Court to reconsider his case. The memo essentially argues that Freshwater has nothing new in his motion for reconsideration, no new evidence or arguments, but is merely a rehash of his previous claims, and therefore it should be denied. It argues on the same grounds on which the Court made its decision, that the... Richard B. Hoppe

WFSU
Maryland Nativity Scene Sparks Atheist Backlash
Christian Broadcasting Network
The scene first went up last year as a community effort by the Hancock Council of Churches. But this year, the Freedom From Religion Foundation complained to town officials about the display. The town manager told the atheist organization the Nativity ...
Atheist Banner Joins Religious Displays At Fla. CapitolWFSU
Atheists Set Up Display at Fla.'s Capitol Building to Combat Nativity SceneChristian Post

all 5 news articles »