I really need more time to fill in a gap in my microbiology education: environmental microbiology. I run across papers all the time that are absolutely fascinating, and wish I had a free year to just take some additional coursework in this area. For instance, a paper in today’s Science magazine discusses how atmospheric bacteria result in the formation of snow.
More over at Aetiology.
Here we have yet another example of evolution cobbling together new proteins from existing structures. And what do you know, it kinda matters:
The TRIM5-CypA gene found in Asian macaques is a hybrid of two existing proteins, TRIM5 and CypA. This combination creates a single protein that blocks infections by lentiviruses.
Continue reading at Neurotopia for more snark.
Answers in Genesis started this so-called peer reviewed journal called Answers, and the latest publication therein is such a confused mess that I'm wondering if it could be a hoax. Just the title alone would be sufficient to tell this is codified lunacy: An Apology and Unification Theory for the Reconciliation of Physical Matter and Metaphysical Cognizance.
Continue reading "Which one of you little rascals Sokaled AiG?" (on Pharyngula)
Tomorrow is the last day to get your Alliance for Science Evolution Essay contest submissions done! You know you want a shot at some money for school books and some free, signed media materials. This year looks to be even better than last, so we look forward to reading what you have to say! Remember, the science teacher for the winning essay writer gets rewarded too, and deservedly so; our teachers work hard and deserve something back.
A while ago I posted an article on Haldane’s Dilemma, in which I pointed out how Mr. ReMine misrepresented Haldane’s work. Now Mr. ReMine has written a response (which I was unaware of until now), in which he claims I misrepresent him.
Unfortunately for Mr. ReMine, the evidence is against him (more below the fold, this article is modified from a comment to this article on the cost of selection).
Nova has made available a professional development course for teachers
This course gives teachers the background and skills they need to counter pressures to present or address religiously based alternatives to the theory of evolution. It is offered for self study or group study, and can be used as a guide for a professional development workshop. It features materials developed for the NOVA program “Judgment Day: Intelligent Design on Trial.”
On Feb 12, I had the opportunity to drop in on some friends in Lexington, Kentucky to help celebrate Darwin Day there. The occasion was the Darwin Day presentation by Dan Phelps (pictured here) entitled “The Anti-Museum: An Overview and Review of the Answers in Genesis Creation Museum”, and the following panel discussion. The presentation was a summation of Dan’s review of the Creation Museum in Northern Kentucky. This review has been published by NCSE, and may be read at the NCSE web site.
Well it looks like one of the minds behind Expelled has joined the Banned in our forum. Go join the discussion and ask him all the questions that the press were not allowed to.
Mr_Christopher Wrote:Hey here is Kevin Miller’s blog I guess he is one of the writers for Expelled? I invited him to drop by and chat with us
I told him most everyone here is an atheist, scientist or evil doer in general. If he shows up please don’t let me down.
Chris!
Never too lazy to do some research when ID creationists seem to be lost for arguments I ran across a paper by Nunney in which he shows how Haldane was wrong. All ReMine supposedly was able to do was to object to the fact that Nunney refused to share the software code with ReMine and that ReMine was unable to write the necessary code himself.
Haldane’s dillema hardly deserves the attention it is receiving from ID creationists but then again, there is not much else for them to focus on.
Nunney’s results differ markedly from those of Haldane and ReMine. Considering Nunney’s reticence to have his results critiqued and the divergence from other results, his results appear to lack credibility.
Enough whine, let’s look at the cheese… (see here for an earlier discussion on the non issue of Haldane’s dilemma by Ian Musgrave).
by Jeremy Mohn
My friends and fellow Kansans Jeremy Mohn and Cheryl Shepherd-Adams (a KCFS Board member) have a nice website/blog called “Stand Up for Real Science” that deserves wider attention. I really like their motto: “Critically Analyze All Theories—Teach the Actual Controversies”
Today Jeremy’s post, Defusing the Religious Issue, takes Discovery Institute fellow John West to task for distorting via quotemine (surprise!) positions held by NCSE’s Genie Scott and by biologist Ken Miller, author of Finding Darwin’s God.
I’d like to post the entire article by Jeremy here. I encourage you to visit Jeremy and Cheryl’s site, and even if you comment here you might drop by there and leave a comment. (By the way, patrons of our discussion forum, After the Bar Closes, will find the first couple of comments there interesting.)
—Jack Krebs
Sometime late this week, I’m going to do some maintenance on the server and this website. I’m going to experiment with enabling compression again. Last time it broke page caching on IE 6. So if you see that this page doesn’t update any next week, then try cleaning out your cache (or use ctlr-r) and see if that fixes the problem. Hopefully, it won’t occur again.
Neil Shubin, author of “Your Inner Fish” can be heard discussing the fascinating story of evolution.
Shubin discusses a variety of strong evidences that support our common ancestry, one in particular caught my eye/ear.
Hiccups…
In a very interesting post, Ian Ramjohn covers some interesting research about the evolution of Bt resistance in cotton pests.
In an article published in Nature Biotechnology, Bruce Tabashnik and colleagues looked at the actual pattern of evolution of resistance to Bt toxin Cry1Ac in cotton over a 10-year period. They used studies conducted in Australia, China, Spain and the United States focusing on six pest species: Helicoverpa armigera, H. zea, Heliothis virescens, Ostrinia nubilalis, Pectinophora gossypiella and Sesamia nonagrioides. They found that in only one of these species - H. zea - had the frequency of resistance genes increased substantially.
Go read the rest at Further Thoughts.
HT: ResearchBlogging.org’s feed, which is becoming an excellent resource.
On Evolution News, Casey Luskin claims that the work by Wired Science to detect the names in the Venter genome sequence is an example of applying a design inference. Indeed, their application of a scientific design inference contrasts strongly with ID’s failed attempts to extend the design inference to include areas of our ignorance.
As is self evident, the example is nothing more than a pattern matching and has no relevance to the design inference approach as proposed by Intelligent Design Creationists which involves eliminating any and all known (and unknown) regularity and/or chance pathways.
It seems that the day when we can detect human intelligent design in biology has come much sooner than expected. But what if there are other sources of intelligent design in biology as well?
According to Rotten Tomatoes, the movie WΔZ starts showing today in the UK. The movie is a psychological thriller/horror movie and has been compared to Se7en. What makes this movie interesting is the fact that the screenplay was inspired by Price’s Equation:
Price’s Equation is a broader version of Fisher’s Fundamental Theorem of Natural Selection. It describes how the change in trait 
with phenotypes 
is related to the phenotypes’ fitnesses, 
. Note that the genetics of the trait (mutation, ploidy, etc.) is contained in the second term. See Wikipedia for more details.
Now according to the Rotten Tomatoes exclusive on WΔZ:
The script comes from City of Vice scribe Clive Bradley, who claims to have come up with the movie’s premise after flicking through a book on Darwinism. “It featured a mathematical equation—W Delta Z—formulated by American population geneticist George R. Price,” he explains. “It supposedly shows that there’s no real altruism in nature; no such thing as selflessness. Price was so upset by his findings that he ended up giving away all his possessions to the poor and, eventually homeless himself, committed suicide with a pair of nail scissors in a filthy London squat.”
The study of the evolution of altruism goes beyond the description above, and I hope moviegoers won’t be seduced by this fictional account of evolutionary theory. (I’m waiting to see what demagoguery that AiG, DI, and the Expelled frauds come up with about this movie.) Now, it is true that according to Price’s Equation, altruistic behavior that benefits a species at the cost of individual fitness is selected against. (Note that a deleterious phenotype can still exist in a population through mutation-selection balance or genetic drift.) However, if the altruism only benefits certain members of the species (e.g. relatives), then altruism can be selected for.
This is represented by Hamilton’s rule: 
. This describes under what conditions an altruistic allele will invade a population. 
is the cost of the allele to the “actor”, 
is the relatedness of the receiver to the actor, and 
is the benefit that the receiver receives by the actor being altruistic. The consequence of Hamilton’s rule is that selfish genes can still be altruistic. There is a lot of interesting literature about the evolution of altruism, including how punishment can reinforce altruism. I recommend Sean Rice’s Evolutionary Theory, Chapter 10, as a good starting point.
So if anyone in the UK goes to see this movie this weekend, please send us an overview/review.
Ever since I read Dembski’s comments on how mathematician Ulam had commented on the low probability of evolution, something kept nagging at me. Familiar with the common creationist affliction of quote mining, I decided to do some additional research.
Remember what Dembski wrote? Ulam wrote in his contribution to the Wistar conference that:
“[Darwinism] seems to require many thousands, perhaps millions, of successive mutations to produce even the easiest complexity we see in life now. It appears, naively at least, that no matter how large the probability of a single mutation is, should it be even as great as one-half, you would get this probability raised to a millionth power, which is so very close to zero that the chances of such a chain seem to be practically non-existent.” (Ulam’s remark on page 21 of the Wistar conference Proceedings.)
As people pointed out already, the phrase, “naively at least”, should have raised some concerns. And for good reasons.
A major problem was my lack of access to the Wistar Monographs, however, Ulam did write a paper soon thereafter in which he revisited some of his earlier work and not surprisingly, the paper paints a very different picture.
On Uncommon Descent Bill Dembski
Evolutionists continue to be much exercised about evolution being treated as “merely a theory,” arguing that to identify it as such is as disreputable as treating gravity or the second law as “merely a theory.” But consider, as a close colleague recently reminded me:
And continues to quote from two scientists, Niels Bohr and Stanislaw Ulam (both physicists)
The new, science-rich edition of the Tangled Bank is hosted by Greg Laden this week. Get your coffee and sit for a while.
Michael Mayo at the Sun-Sentinel exposes the real issues behind the opposition to the new Florida Science standards
“Evolution is just another one of Satan’s lies to get people to believe there is no God,” Laura Lopez, a mother of three from West Palm Beach who opposes the proposed new standards, told my colleague Marc Freeman.
As a Christian and a scientist, I find the continued ignorance portrayed by fellow Christians to be painful. How can it be that they have been led so astray that they are willing to undermine Christian faith with their foolish words?
Today, the Florida Board of Education met. One of the items on the agenda: the proposed new science standards. These were politically controversial because they included “evolution” and benchmarks concerning concepts in evolutionary biology.
The Board decided last week to allow a limited amount of public comment at this meeting. I have a brief description of how that went down, modulo the poor webcast availability, at my weblog.
The consideration is ongoing now. I’ll update this later today.
OK, it’s over. Florida adopted amended standards. We know from prior experience that when one agrees to language from the anti-science advocates, they have some angle for exploitation of that language. While Florida standards now do mandate the teaching of evolutionary science, they also have the antievolution back-door installed. There will be further years of dealing with antievolution efforts in Florida because of this action.
I really should have loved Michael Shermer’s The Mind of The Market, because I am not only a libertarian but also fascinated by evolution and its scientific, economic, and philosophical implications. Moreover, I believe sociobiology can provide extremely important insights that offer a grounding for political philosophy on a genuine, objective human nature. And yet I found the book disappointing and even unconvincing. It is chock full of the hasty generalizations and oversimplifications that have led so many people to keep sociobiology at arm’s length. A good science-based defense of libertarianism will have to be much more rigorous than this.
Since I wrote about the wacky creationist who couldn't wrap his mind around the idea that plants and animals are related, and since I generally do a poor job of discussing that important kingdom of the plants (I admit it, I'm a metazoan bigot…but I do try to overcome my biases), I thought I'd briefly mention an older review by Elliot Meyerowitz that compares developmental processes in plants and animals. The main message is that developmental processes, the mechanisms that assemble the multicellular whole, are very different in the two groups and are non-homologous, but don't get confused: the basic cellular processes are homologous, and there's no doubt that we are related. The emphasis in this paper, though, is the evidence that plants and animals independently evolved multicellular developmental strategies. There is some convergence, but the tools in the toolbox are different.
Continue reading "Plant and animal development compared" (on Pharyngula)
PT readers may be interested to check out this great new article in New Scientist, which reviews recent developments in flagellum evolution. The thing I find interesting about all this is how the IDists have been intellectually unable to concede any tiny little mistake in anything they said, e.g. this standard ID argument from DI fellow Bruce Gordon as it was presented in 2006:
Our friends at Florida Citizens for Science report on a variety of positive developments. All this may very well be related to the public hearing in which so many creationists got to demonstrate the deep level of ignorance amongst the public when it comes to evolution and evolutionary theory.
1. Monroe County approves resolution in favor of the proposed standards
2. The American Institute of Biological Sciences has released a letter in support of the standards
3. Americans United for Separation of Church and State released a letter in support of the standards
4. The Florida Academy of Sciences presented a supporting resolution during the Monday public forum meeting in Orlando.
5. The members of the writing committees have sent a letter of support to the Board of Education.
HT: Nate for providing an updated version of the Florida map
Today is Darwin Day. Get out and learn some biology!
If you have links to Darwin Day events or posts, send them in. There is also a Darwin Day carnival being run by ScientificBlogging.com.
There was a meeting held in Orlando, Florida today to allow public comment on the proposed new Florida science standards. The new standards incorporate evolution, both word and concept, into the benchmarks. That sort of thing might cause a Bill Buckingham to exclaim, “It’s laced… with Darwinism!” And it pretty much did.
I spent a fair amount of time between 10 AM and 2:30 PM today listening to the webcast of the event, when it was working. (The remainder I used tending Diane, who has the flu.) The event ran from 10 to 3:30, so I heard most of it.
I have a retrospective overview at my weblog:
Barring any media bombshells, the public commentary phase of responses to the proposed Florida science standards is now over and done with. I have not yet seen every minute of the meeting today in Orlando, but I did sample several hours of it.
There are several things to be said. The first is that I am very proud of the leadership role that the Florida Citizens for Science group played in bringing things to this point. While the pro-science side was numerically under-represented among the commenters, I recognized many of them as members of Florida Citizens for Science. Among those, FL CfS President Joe Wolf presented the petition supporting the standards that so many of you have signed, noting the total number collected in less than two weeks as over 1,500 signatures, and that somewhat more than 1,000 of those were Florida citizens. FL CfS Treasurer Pete Dunkelberg made excellent use of his three minutes at the podium, reminding the Florida Board of Education that they have the opportunity to change Florida’s standards score from “F” to “A” – if only they don’t mess up at the last minute by capitulating to the anti-science crowd.
Read here for more.
I also have a series of posts from summarizing various speakers while the webcast ran:
Part 1 Part 2 Part 3 Part 4 Part 5 Part 6 Part 7 Part 8 Part 9
Comment either here, there, or at After the Bar Closes.
History has a tendency to repeat itself. In an effort to control the language of the debate, communications consultant Frank Luntz wrote a memo in 2001 advising Republicans how to control the language of climate change:
“The scientific debate remains open,” he wrote , “Voters believe that there is no consensus about global warming within the scientific community. Should the public come to believe the scientific issues are settled, their views about global warming will change accordingly. Therefore, you need to continue to make the lack of scientific certainty a primary issue in the debate, and defer to scientists and other experts in the field”
We observe a same lack of appreciation of science by voters on the topic of evolution. Let’s explore some of these similarities and see what we can learn from them.
Yesterday a really cool paper came out in the journal Nature that demonstrates why evolutionary theory is so useful and fruitful in biology. A team of researchers has recreated an ancestral bacterial protein to determine that the ancestral bacteria grew in hot water around 3.5 billion years ago.
The Board of Regents met to hear Gonzalez’s appeal this morning. It’s worth noting that they rarely take a differing view on tenure decisions from the tenure committee itself. So sorry Tara, you got it wrong… the decision is already out, and it’s not a shocker:
The Iowa Board of Regents has denied Guillermo Gonzales’, associate professor of physics and astronomy, appeal for tenure. After a private deliberation, the Board voted down the appeal which has already been denied by Iowa State University and ISU President Gregory Geoffroy.
No details at this point. But look for the Discovery Institute Spin Room to start kvetching at any moment, if they haven’t already. At least Casey Luskin will have something to whine about besides his inability to figure out internet image copyright stuff. Might I suggest that he just pretend that Gonzalez was actually thrice denied tenure– once by the tenure board, once by the Preznident, and once by the Board of Regents– for maximum martyrhood?
It’s practically Biblical.
Edit in: A more detailed news release can be found here
It’s not certain there will be a decision immediately, though:
The Iowa Board of Regents will meet Thursday to discuss the tenure denial appeal of Guillermo Gonzalez, assistant professor of physics and astronomy at Iowa State, at its regional meeting on the ISU campus.
The meeting is at 8:30 a.m., with a one-hour closed session dedicated to discussing the appeal beginning at 8:35 a.m. The regents will emerge with either a decision on the case or a decision to postpone it.
“The board does not have to decide within the hour time slot given for the meeting, and discussion may take place over the following days,” said Iowa Board of Regents President David Miles.
Stay tuned…
Our friends at Florida Citizens for Science mention some good news in Florida:
Make that two for the science standards - A second Board of Education member has come out in favor of solid science education.
Highland County resolution fails
Read also this story
Concerning the proposed resolution and the teaching of alternative theories, he asked the board, “what theories are you advocating being presented in the scientific curriculum?”
After a pause, Hancock replied, “I don’t think you are going to get that answer.”
Broen said, “since the resolution states there are other theories to be presented to the student, yet the board members have failed to produce them, then it seems this resolution must be discarded.”
Someone is realizing that there are no alternative theories…
We’re now into the third day of the brouhaha that was sparked by Casey Luskin’s misuse of the “Blogging About Peer-Reviewed Research” icon. Casey posted a few responses to criticisms in the discussion thread over at the BPR3 blog, then packed his bags and went home because Dave Munger didn’t delete all of the comments that had said bad things about Casey. It’s pretty clear that Casey got what he was fishing for before he left, though: more stories about how poor Intelligent Design proponents are picked on by mean scientists.
They’ve been playing up that sort of story for a while now, and it’s easy to understand why. Stories - even blatantly fictional ones - are a good way to make a point. We use stories to teach our children. More importantly, our parents used stories to teach us. We’ve been dealing with stories all our life, so we tend to respond when we’re given a familiar story. In this case, they’re giving us a variant of the “David and Goliath” story, and we all know who to root for when we hear that one, right?
Casey had to work really hard to get that story, but he’s pretty sure he managed it:
(1) A large number of the people on this thread continue to oppose approving my request for registration, explicitly admitting that they simply don’t want to allow ID proponents to be part of these discussions. If ID proponents aren’t even allowed to “officially” blog about peer-reviewed research on the internet, who can say that their research would get a fair hearing from the actual peer-reviewers in the real world of science?
The italics were in the original, and Casey really must have meant it, because he used the same phrase again later on in the comment, replacing the italics with boldface. As arguments go, that one is pretty typical. It sounds nice and reasonable and bears only the faintest resemblance to anything that actually happened.
Read more at The Questionable Authority, where comments may be left:
by Daniel Brooks
Following is a guest post by Daniel R. Brooks, FRSC. Brooks is a professor in the Department of Ecology & Evolutionary Biology at the University of Toronto. In June 2007 he attended an apparently secret conference organized by ID advocates and entitled the “Wistar Retrospective Symposium.”
This is a reference to an obscure 1966 Wistar Institute symposium which became famous in creationist circles (just read the 2000+ google hits on “wistar creationism”) for allegedly being the place where mathematicians demonstrated the unworkability of evolution by natural selection. If one actually reads the conference transcript, one realizes that what really happened was that approximately two befuddled math/computer science people, Murray Eden and Marcel-Paul Schützenberger (who was later a longtime friend/collaborator of David Berlinski, by the way), were schooled in basic population genetics & evolutionary theory by the likes of Ernst Mayr and Sewall Wright. It makes hilarious reading, along the lines of “we biologists worked out this math 40 years ago, why haven’t you read up on it” and “I can’t get my particular evolution simulation to work on my 1960s-era computer, therefore something is wrong with evolutionary theory!” The central misunderstandings from the mathematician side involved, as always, the same old dumb “but it’s impossible/extremely improbable for these sequences to come together all at once by random chance!” argument, which ignores (as always) the elemental point that evolutionary theory is the exact opposite of all-at-once-by-chance assembly.
I entered a comment when I signed the Florida Citizens for Science online petition in support of the proposed new science standards there.
I was born in Florida, and I care about the state of science education there. There are two main things that I want to say about antievolution and science education.
First, antievolution is not based in science, does not represent an alternative scientific understanding of the evidence, and it specifically conveys a narrowly sectarian religious doctrine. It is disruptive of the tolerance towards diverse religious faiths, or the lack of them, that help maintain amity and civility in our country. We are fortunate here to have avoided the deadly struggles over doctrinal positions that are common elsewhere and that have left their stamp on history. Antievolution efforts include attempts to rewrite the operating principles of science by fiat, and this alone should be sufficient to demonstrate that its promoters are not working for the common weal, but are bent upon achieving their own aims without regard for anything but their own satisfaction.
Second, science education needs to incorporate those concepts that have accountability, that have been proposed, argued, tested, revised, and that have by the record of empirical investigation and substantial engagement of criticism convinced the scientific community of the worth of the concept in question. Evolutionary science has met that high standard, and antievolutionary attacks upon it have no such claim to legitimacy. Science education should not be weakened by spending precious class time on material whose inclusion only serves the purposes of evading those stringent standards of accountability, undermining the principle of science’s ability to wholly reject hypotheses that predict false consequences, and gainsaying well-tested theories without substantiating a basis for such attacks.
It can do no one harm to come to an accurate understanding of what science is, and what has been discovered and supported through the scientific method. Please adopt the new science standards as written by your domain experts and experts in science education, and avoid the error of capitulating to the demands of the antievolution movement that evolutionary science be “balanced” with material that sows broad distrust of scientists and findings in biology, chemistry, physics, astronomy, and geology.
This thread is for comments sent to the online petition only. Let’s keep things tidy; I’ll remove comments that have extraneous remarks to the Bathroom Wall.