August 2011 Archives

Carnival of Evolution 39

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CoEButton.jpgThe 39th Edition of the Carnival of Evolution awaits your arrival at The End Of The Pier Show.

This lovingly prepared version includes nematodes, spider mites, mimiviruses and some information about an odd genus called Homo. Don’t miss great entries from the BEACON Center for the Study of Evolution in Action.

It’s a very nice edition of an excellent carnival. Click on over.

On August 15, The New Yorker published an article by Ryan Lizza asserting that Republican presidential candidate Michelle Bachmann was influenced by “Dominionism”, via fundamentalist theologian Francis Schaeffer and one-time Schaeffer student Nancy Pearcey. “Dominionism” as it is being used here, refers to Christian Reconstructionism, the idea that old-fashioned Old Testament Biblical Law should become U.S. law, a position usually associated with Rousas John Rushdoony.

We have have met Nancy Pearcey before; amongst other things, she is a current ID proponent and Discovery Institute fellow. Back when it was still cool to cop to being a creationist, though, she was a longtime editor of the young-earth creationist Bible-Science Newsletter, endorsed the idea that humans lived with dinosaurs, and was a coauthor of the first ID book, Of Pandas and People. For documentation, see my 2006 PT post Yet another version of the origins of ID and, for the publication of much of Pearcey’s chapter of Pandas in the Bible-Science Newsletter, see my 2005 PT post Why didn’t they tell us?

Pearcey authored the 2004 book Total Truth (forward by Phillip L. Johnson, remember him?), and Michelle Bachmann recommended the book, providing Ryan Lizza his link:

If you decided not to enjoy the Ramachandran lecture when you saw that it was in a format that reminded you of Windows 3.1, I have good news. The post has been updated with links to the new Reith Lectures site at the BBC, and now you can listen to the lecture in your browser or download it as a podcast.

It’s great stuff, so don’t miss it. Oh, and send me nominations for future BILLs. The email address is BILL at pandasthumb dot org.

Party on!

We received approximately 40 photographs from 20 photographers. Most of the pictures were excellent. We divided the entries into 3 categories, Land, Sea, and Sky, though we had to fudge a little bit to populate all 3 categories.

Choosing finalists was difficult. We considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for style.

Here are the finalists in the Sea category. Please look through them before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The winner in each category will receive a copy of The Way of the Panda, by Henry Nicholls; we thank the publisher, Pegasus Books, for their generosity in providing the books.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

The winner of the Land category, with 34 out of 78 votes, is Cooling pahoehoe lava, by Andrew Cooper. Nicholas Plummer came in second and Lynn Wilhelm, third. Finalists in the Sea category will be posted shortly. Congratulations to everyone who participated.

Wanna demonstrate how evolution and scaffolding can produce irreducibly complex structures at your next ivory tower wine and cheese party or evil atheist conspiracy kitten roast? Just repeat the demonstration seen in this clip.

(HT: Nick Matzke.)

Last Chance to Vote

We’ve fixed the problems with logging in to vote!

We need your vote on the third edition of our Photography Contest. Voting ends this weekend.

Just go here to view the finalists and vote.

You have to sign in to vote, but it’s easy. We accept local accounts and Facebook, Google, Yahoo, etc. accounts.

[Republished from Homologous Legs]

The intelligent design (ID) movement has been around for over 20 years, and few (if any) of its stated and implied goals and plans have thus far come to fruition. While contributing factors to this lack of success are certainly the hard work of the scientific community and its friends, as well as the fact that ID has never been adequately formulated as a scientific idea, a significant proportion of the responsibility for the outcome should be laid upon the ID movement itself. It has, in arguably many respects, acted in the exact opposite way that it should have acted if it wanted to be taken seriously - only one example of which is bringing up religion whilst simultaneously claiming that they weren’t and then chastising critics who pointed out what they were doing.

It’s hard to find an ID proponent who will admit this. Like many movements, the one constructed around ID is insular, mistrusting and lacks introspection, and it spends most of its time on attacking “the Darwinist enemy” in academia instead of really thinking about what it’s doing. This is understandable, considering it’s been relentlessly criticised by the scientific community ever since it poked its head up out of the carcass of creation science, rendering it in a somewhat-perpetual state of defensiveness. Those few proponents who can somehow forget the fact that nearly every biologist in the world would laugh about their ideas to their face given the chance still attack evolutionary biology with unparalleled confidence, which bolsters the morale of those in the Internet trenches: and thus the movement continues. Even with its “Darwinist conspiracy” mindset, it still thinks it’s winning. But it’s not. Not by a long shot.

Epigenetics is the study of changes to DNA molecules that do not involve mutations or the changing of nucleotides. Currently, epigenetics seemed to have surpassed the related field of developmental biology as staking claim to being the new revolution in evolution. (IDists, you still have a way to go to become a scientific fad. You gotta drop the bullhorn and start doing some science.)

I’m with Jerry Coyne; call me unfashionable, but my response to these fads is “meh.” In fact, Dr. Coyne has done a great job in discussing why these findings make evolutionary biology more wondrous, but don’t disrupt evolutionary biology or the central place of Darwin’s theory of natural selection has in it.

Dr. Coyne places the blame of these fads on science journalists, but I would go further and place additional blame on scientists themselves. It is my opinion, that much of this “Darwin to the doghouse” rhetoric begins with the scientists, specifically ones who have no background in evolutionary biology—say biophysicists or molecular biologists with a mostly biochemistry background. These are the ones who are likely to have just enough knowledge to think they understand evolution, and thus are mistakenly confident to say that they are overturning it. (And I shouldn’t forget the physicists and engineers, who always know better than us “soft” scientists.)

These people exist because many college programs in the biological sciences don’t even require a course in evolutionary biology. (Seriously! Are they afraid that the pre-meds will revolt?) Until that changes, we will still be training too many biologists and physicians whose knowledge about evolution is gathered more from television than the classroom.

Please Vote if You Haven’t Yet

We need your vote on the third edition of our Photography Contest. Voting ends this weekend.

Just go here to view the finalists and vote.

You have to sign in to vote, but it’s easy. We accept local accounts and Facebook, Google, Yahoo, etc. accounts.

Bill&Ted2Crop.jpgUPDATE: Links are now changed to take you to the newer BBC site, on which you can listen to the lecture without the hassle of getting RealPlayer. And you can download the lecture as a podcast if you prefer.

The third BILL is a brilliant foray into neuroscience, focused on consciousness and the human brain.

BILL the third is “Synapses and the Self,” by Vilayanur S. Ramachandran. Ramachandran is the author of Phantoms in the Brain (1999) and most recently of The Tell-Tale Brain: A Neuroscientist’s Quest for What Makes Us Human, published this year.

This lecture is audio only, accompanied by a transcript. It was the second in Ramachandran’s five-lecture series “The Emerging Mind,” which was the 2003 installment in the fantastic Reith Lectures. All five lectures are riveting; this one includes some thoughts on human evolution and might thereby ensnare many Panda’s Thumb regulars. If you can’t get enough of Ramachandran after this introduction, you’ll find videos of other lectures and a NOVA appearance on the ‘tubes. And he blogs a bit; the most recent entries discuss his remembrances of Francis Crick.

I encourage you to listen without referring to the transcript; he’s very clear and fun to listen to.

When I was in grad school at the University of Georgia, I participated in a case concerning the teaching of evolution: Selman v. Cobb County School District. The case revolved around a disclaimer that the affluent Cobb Country (Georgia) School Board affixed to biology textbooks.

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered.

And for those of you who don’t remember, the county lost:

The critical language of the Sticker that supports the conclusion that the Sticker runs afoul of the Establishment Clause is the statement that “[e]volution is a theory, not a fact, concerning the origin of living things.” This statement is not problematic because of its truth or falsity, although testimony from various witnesses at trial and the amicus brief submitted by the Colorado Citizens for Science, et al. [That’s us!], suggest that the statement is not entirely accurate. Rather, the first problem with this language is that there has been a lengthy debate between advocates of evolution and proponents of religious theories of origin specifically concerning whether evolution should be taught as a fact or as a theory, and the School Board appears to have sided with the proponents of religious theories of origin in violation of the Establishment Clause.

As you can see, an important part of the case hinged on the misleading language of the disclaimer. (The state of Alabama is still slapping similar disclaimers on books.) So it is great to see that Larry Moran has updated his article, “Evolution Is a Fact and a Theory” and posted it on his blog. Of course, it’s unfortunate that we still have to make this point because some people never get it.

Over at Uncommon Descent, Eric Holloway has declared that the critics of William Dembski’s 2002 book No Free Lunch actually accept that the No Free Lunch Theorem applies to evolution. He uses as his evidence the replies to Dembski’s use of the NFLT by Allen Orr and by David Wolpert (who co-wrote the original NFL paper). They had argued that evolution was a more complicated process than the simple model used in the NFLT, a model that for evolution would associate fitnesses with genotypes in a simple search for the genotype of highest fitness. So aren’t computer scientists (Wolpert) and biologists (Orr) implicitly acknowledging that the NFLT theorem applies to any such simple model, and prevents it from searching effectively?

But there have been other criticisms of Dembski’s use of the NFLT, and Holloway does not cite them. I summarized them in a 2007 article I wrote in Reports of the National Center for Science Education. And in the matter of the use of the NFLT my criticisms were actually not new — as I noted there, the fundamental point had been made many times since 2002, originally in a 2002 article by Richard Wein, and also in articles by Jason Rosenhouse (2002), Mark Perakh (2003), Jeffrey Shallit and Wesley Elsberry (2004), Erik Tellgren (2005), and Olle Häggström (2007). I will immodestly claim that my article is the clearest of these many clear articles.

So what is this oft-repeated criticism? When we have a simple model of evolution with genotypes and phenotypes, the NFLT argues that if we average over all the ways that set of fitnesses could be associated with the genotypes, that a simple model of search that climbs uphill on the fitness surface cannot do any better than a random search by pure mutation (one which is unaided by natural selection). That is disastrously bad. It sounds like it says that natural selection in such a model cannot work at all.

But notice the averaging part. It is critical to Wolpert and Macready’s theorem. In effect, it says that we are dealing with an infinitely rough fitness surface. If we change a genotype by making one mutation — changing a single position in its DNA — we arrive at a genotype whose fitness is randomly chosen from the whole set of possible fitnesses. In effect, a single mutation has the same effect as mutating every site in the genome simultaneously. (I apologize for shouting, but the point is not being noticed over at UD).

Of course real biology doesn’t work like this. Mutations are on average worse, but they mostly don’t instantly reduce the organism to rubble. In the real world, nearby genotypes are usually similar in fitness — often a bit worse but sometimes a bit better. In the NFLT world essentially all mutations are disastrous, and evolution would not work. So the No Free Lunch Theorem does not model real biology, not even in a simple model of evolution searching for genotypes of higher fitness on a fitness surface.

So far Holloway has not cited any of these criticisms, and when asked by a polite commenter whether there are any such criticisms, he has simply declared that

I spent some time reading the critics, and this bore [sic] my frustration. I could not find one author who treated Dembski’s work fairly! If someone could fairly refute Dembski’s work I’d be all over it, but I haven’t found anyone! Instead its all passive aggressive ad homineum [sic] and brow beating, with ample burning of strawmen, very tiring to read.

So the discussion at UD continues, hermetically sealed in a self-reinforcing bubble (though I notice now that in that discussion Elizabeth Liddle has tried to raise the relevant point).

Note added 8/29/2011: Eric Holloway has now replied to this post in a post he made recently at Uncommon Descent. For my response to this reply, see the two comments I have made below dated 8/29/2011 at 1:17am and the one following that.

As many of you know by now, about two weeks ago a movement took shape on the Internet to get the Montreal authorities to actually get involved with the prolific spammer of death threads, “David Mabus/Dennis Markuze.” Finally, last week he was arrested and charged with 16 crimes and is currently undergoing a psych evaluation for 30 days.

Tim Farley has written a wondrous account of the entire campaign. I’ll give a summary below, but you need to read the whole thing.

Like most evolution/skeptic websites, we have experienced the death threats of Mabus first hand.—I’m sure readers can find ones that have not been deleted from our archives.—I think he eventually went away after we got our filters configured in such a way that he was unable to figure out a way around them. We were still on his mailing list until earlier this year when he decided to move his operation to Twitter. It turns out that Twitter was his downfall.

Complaints about Mabus’s death threats have been lodged many times over the years, but the Montreal police never acted on them because nearly everyone he threaten lived somewhere else. However, it was on Twitter that Montrealer William Raillant-Clark discovered Mabus’s threats. And in the course of trying to do something about the appalling behavior became noticed by Mabus and started receiving death threats in turn. Unfortunately for Mabus, Raillant-Clark had brought the Montreal police into the conversation, who responded with the email address of their public relations division. Raillant-Clark’s efforts also caught the attention of Kyle VanderBeek, who started a petition for the Montreal Police to take Mabus seriously. It received over 5,000 votes, each one generating an email that was sent to the address tweeted by the department. (They eventually cried “oncle.”)

Now on Twitter, Mabus would auto-harass anyone who mentioned or was mentioned by someone he was already harassing. Thus when the Montreal Police tweeted their email address to Raillant-Clark, Mabus began automatically harassing it too.

Thus Mabus was sending death threats to a fellow Montrealer and CCing the police to his plans.

There needs to be a new FAIL smiley/icon for this.

The Oxford English Dictionary defines “taxonomy” as “classification, esp. in relation to its general laws or principles; that department of science, or of a particular science or subject, which consists in or relates to classification; esp. the systematic classification of living organisms.” Without a doubt, taxonomy is a major arm of biology.

A taxonomist and collaborator of mine, Brendan Hodkinson, recently opined on the status of taxonomy as an art or a science.

I tend to think of science itself in a very strict sense, as the process of developing and testing hypotheses. However, my big caveat is that there are many activities that are involved in (and are absolutely essential to) the practice of science that are not science per se according to that definition. This does not diminish their value to science. Some of this has to do with the acquisition of background knowledge that informs the hypotheses to be tested, while some of it is associated with making the results of inquiry available and comprehensible to the scientific community and the public.

So then is taxonomy art or science? …

Read the rest to see his conclusion.

We received approximately 40 photographs from 20 photographers. Most of the pictures were excellent. We divided the entries into 3 categories, Land, Sea, and Sky, though we had to fudge a little bit to populate all 3 categories.

Choosing finalists was difficult. We considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for style.

Here are the finalists in the Land category. Please look through them before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The winner in each category will receive a copy of The Way of the Panda, by Henry Nicholls; we thank the publisher, Pegasus Books, for their generosity in providing the books.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

Over at Science, Food, Etc. Mohamed offers an intentionally hyperbolic list of faculty stereotypes. He is looking for stereotypes that are missing from his list. So lets help him out. Here are some of his examples.

HALL-TALKER: Prof you never see actually doing work, but seems to be always standing in the hall (or worse, in your office) talking. Seems to even roam the halls trying to find the next person with whom to talk.

ABSENTEE: Prof who is either traveling or works from home so much that most of their colleagues forget that they even work there. Their students may have forgotten them, too. Everyone looks startled when they walk into their laboratory or into a faculty meeting– “Who is that?” someone asks.

Go have fun and read the rest.

Guest commentary by Dan Phelps, [Enable javascript to see this email address.].

On the evening of August 9, 2011, the City of Williamstown, Grant County, Kentucky, and Ark Encounter (AE)/Answers in Genesis (AIG) held a “Listening Session” at Williamstown High School to discuss local concerns about the Ark Park. Government officials present included Williamstown Mayor Rick Skinner, the entire Williamstown City Council, members of the Dry Ridge City Council, Wade Gutman of the Grant County Industrial Board, Sally Skinner of the Williamstown Independent School Board, members of the Grant County School Board, the Grant County Planning Board, the Grant County Tourism Board, the Rural Development Board, Royce Adams of the Kentucky House of Representatives, a representative of the Veteran’s Cemetery, and Judge Executive Darrell Link of the Grant County Fiscal Court. Representing Ark Encounter/AIG were Mike Zovath and attorney Jim Parsons. Tad Long of the Kentucky League of Cities served as a facilitator. The local cable access channel videotaped the meeting. I made an audio recording.

Approximately 450 to 500 citizens attended the meeting; all seats were taken and a number of people had to stand along the walls. Interestingly, the majority of attendees appeared to be forty or older. The event was well organized and friendly throughout. Mayor Skinner briefly introduced the various people giving presentations and those available to answer questions.

As many of you may recall, I developed a population genetics simulation for PT called Red Lynx (available here and here). I know that several people are using it in the classroom, and I would appreciate some feedback. Just drop me a line ([Enable javascript to see this email address.]) or post a comment letting me know where it is being used and in what class. I’d also like any feedback on how students enjoy it.

Thanks ahead of time.

Over on the DI blog, David Klinghoffer wrote:

Darwinists on RNA World: “No Comment” David Klinghoffer August 19, 2011 6:00 AM | Permalink

Darwinists routinely complain about our policy on comments here: we allow them when we do, and don’t when we don’t. The impression is that they are just itching to have at our science writers. Yet we opened comments the other day on Jonathan M.’s thoughtful take-down of the RNA World hypothesis as a solution to the origins-of-life conundrum – and no critics showed up for the party. Only friendlies did so. Come on, gentlemen! Jonathan’s conclusion:

Michael Marshall’s New Scientist article does not even come close to demonstrating the feasibility of the RNA world hypothesis, much less the origin of the sequence-specific information necessary for even the simplest of biological systems. Since information is a phenomenon uniformly associated with intelligent causes, it follows inductively that intelligent design constitutes the best – most causally sufficient – explanation for the information-content of the hereditary molecules DNA and RNA.

Go there and let us know why you disagree.

Hmm, that’s quite odd, since I’ve been commenting on JonathanM’s pieces occasionally over the last few weeks, mostly at Uncommon Descent.

Intelligent design news and discussion for August 10th to August 18th, 2011.

This week, the Discovery Institute did something rather strange. Well, actually, it’s been leading up to it for a while, but it was only in the last week that this trend became completely apparent: Evolution News & Views, its main blog, is now devoting serious amounts of space in its written output to posts on religion and atheism. Often these posts have seemingly little or nothing to do with the stated purpose of the blog, which is to “[provide] original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research”:  it’s had a “Faith and Science” category for a while now, but the intensity of posts has reached a somewhat amusing level, most of them coming from the supernaturally-inclined mind of DI Senior Fellow David Klinghoffer.

So, in this edition of TWiID, I’ll be touching on many of the religious posts over the last week on ENV, as well as more on the bacterial flagellum (again!) and the supposed design and inspired beauty of butterfly wings.

Changes at NSF

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The biology proposal cycle at NSF is going to be changed into an annual cycle of preliminary and full proposals. The assistant director has detailed the changes in a letter to scientists.

August 15, 2011

Dear Colleague:

As you are no doubt aware, the proposal workload across the Foundation has increased dramatically over the past decade. For example in IOS, the number of unsolicited proposals received into the core programs during this time period has increased 43% while the number of awards made has decreased by 11 percentage points, from 28% to 17%. Clearly, this is a burden on the Program Directors and administrative staff at NSF as well as on the community, who, in addition to submitting proposals are also called upon to serve as ad hoc and panel reviewers.

Effective immediately, the Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) has initiated new procedures for the submission and review of regular research proposals to the core programs within the Division of Molecular and Cellular Biosciences (MCB), Division of Environmental Biology (DEB), and Division of Integrative Organismal Systems (IOS). One goal of these new procedures is to reduce the burdens on the PI and reviewer communities associated with intensifying competition for limited funds. A second is to better manage proposal processing in the face of growing proposal submission numbers while maintaining the high quality of the merit review process and resulting funding selections 1. In response to these challenges, three BIO Divisions are revising their procedures for submission and review of research proposals. The changes for MCB were previously announced in a new solicitation (NSF-11-545).

DEB and IOS will both implement an annual cycle of preliminary and full proposals beginning in January 2012. Preliminary proposals will be accepted in January. Following review by a panel of outside experts, each applicant will be notified of a binding decision to Invite or Not Invite submission of a full proposal. Please note that each investigator is limited to submitting two preliminary proposals a year to either Division, whether as a PI, co-PI or lead senior investigator of a subaward.

All proposals submitted to DEB or IOS in response to the core program solicitations, and to the Research at Undergraduate Institutions (RUI) and Long-term Research in Environmental Biology (LTREB) solicitations, must pass the preliminary proposal stage. The only exceptions are LTREB Renewals.

RAPIDs, EAGERs, conferences/workshops and supplemental funding requests will continue to be accepted at any time by IOS and DEB programs. Proposals submitted in response to special solicitations (e.g. BREAD, CAREER, CNH, EEID) will remain unaffected by these new review procedures. However, OPUS and RCN proposals will only be accepted by the core programs in DEB and IOS once a year at the August deadline for full proposals.

Full details can be found in a new Program Solicitation that will be posted on each Division’s website (DEB) and (IOS) . A single set of Frequently Asked Questions (FAQs) about these changes also can be found at http://www.nsf.gov/publications/pub[…]key=nsf11079 and linked from each Division website. In addition, both IOS and DEB will be hosting webinars to provide further information, please see the Division websites for details and contact information if you have questions or concerns.

Sincerely,
Dr. Joann Roskoski
Assistant Director (Acting)
Directorate for Biological Sciences

Badlands National Park

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Photograph by Alexandra Young.

Rainbow over Badlands NP SD by Alex Young.jpg

Rainbow over Badlands National Park, South Dakota.

Magnificent momma

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This is one beautiful plesiosaur, Polycotylus latippinus.

Polycotylus.jpeg
(Click for larger image)

(A) Photograph and (B) interpretive drawing of LACM 129639, as mounted. Adult elements are light brown, embryonic material is dark brown, and reconstructed bones are white. lc indicates left coracoid; lf, left femur; lh, left humerus; li, left ischium; lp, left pubis; rc, right coracoid; rf, right femur; rh, right humerus; ri, right ischium; and rp, right pubis.

Well, no, not really, but a recent program on National Public Radio in the U. S. claimed that “Evangelicals Question the Existence of Adam and Eve.” More specifically, the program noted that Dennis Venema of Trinity Western University and a few other evangelical scholars argue, correctly, that evolutionary theory precludes the possibility that all of humanity descended from a single couple. Let us hope that they are the thin edge of the wedge.

Unfortunately, the bottom line is more likely a statement by Albert Mohler, the president of Southern Baptist Theological Seminary: “Without Adam, the work of Christ makes no sense whatsoever in Paul’s description of the Gospel .…” I have no idea whether this claim is true, but it is certainly not evidence for the existence of Adam. Venema and the others are on the right track when they note that the Bible consists of allegory and poetry, as well as history, and need not be taken literally. Mohler, by contrast, needs to learn the meaning of the phrase begging the question.

Yahoo Logins

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For those of you using Yahoo logins to comment, you can customize your displayed username by going to Yahoo.com > Account Information > Manage/Create OpenID > Show customization options. By doing this, you can get rid of those ugly urls in your username.

Update

If you have already signed in with a Yahoo account, you need to remove the PT entry under “Manage App and Website Connections” from your Yahoo account settings. Then when you sign it again, Yahoo will ask you to pick which OpenID identifier you want to use.

Springboro Update 2

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I’ve seen a report originating with an anonymous member of the public who attended the Springboro Board of Education meeting on Tuesday of this week. According to the report, approximately 12 members of the public, including at least one representative of the local teachers union, spoke against the proposal to explore including creationism in the Springboro school curriculum. No one spoke in favor of the proposal, and at least one board member was reported to have claimed that the whole thing was taken out of context and that they were just asking questions. It appears that the board is moving on, abandoning the issue at least for the time being.

Mark Pallen (of Pallen and Matzke fame) offers an interesting take on on the Minimum requirements for a PhD thesis.

I am getting tired of having to examine sub-standard PhD theses and then having to write the same old comments in the report on the thesis, so I have decided to set down the minimum requirements for a PhD thesis. Anyone who is contemplating asking me to examine a thesis should read these and comply with them or stop wasting my time. And be warned, you don’t want to get me cross by wasting my time with substandard theses that are an insult to my intelligence!

All you grad students out there need to take note of his advice.

Bill&Ted2Crop.jpgThe second BILL is an entertaining and accessible introduction to evolution, with a focus on Mr. Darwin himself.

BILL the second is “Endless Forms Most Beautiful,” by Sean Carroll. (Not the cosmologist or the biologist formerly in Joe Thornton’s lab and currently at Harvard, but the evo-devo thinker who is Vice President for Science Education at the Howard Hughes Medical Institute [HHMI].) Carroll’s talk is the first in a four-part series on evolution, the 2005 Holiday Lectures sponsored by HHMI. The Holiday Lectures are probably an exaptation of The Royal Institution Christmas Lectures that gave us our inaugural BILL.

Here are some things to look for and think about:

  • An extensive historical account of Darwin’s thought, including some questions about the reactions of his family.
  • An emphasis on the fossil record.
  • A very interesting choice of an experimental study to illustrate natural selection: coat color in pocket mice. Why interesting? It’s the work of Hopi Hoekstra, coauthor of a harsh critique of evo-devo that started a quaint little scientific dustup. (The article and dustup were a couple years after the lecture. More at Pharyngula.)
  • Some simple math to show the reasonableness of evolutionary change over actual time scales.
  • Good questions from the audience, about how the mutations got there in the first place and whether the changes are a “coincidence.”

Intelligent design news and discussion for July 1st to August 9th, 2011.

Did the ID movement miss me whilst I was gone? Maybe, maybe not. I don’t pretend to believe I’m important enough to be noticed, so I’ll leave that there. But then again, I don’t blog to necessarily be noticed and to directly engage with the ID crowd: I blog in order to disseminate correct information and to share a passion for science and demonstrable truth (as tacky as that phrase is - I apologise).

So, yes, this is a TWiID that encompasses a little over a month of pro-ID blog posts. As usual, only the most interesting ones will be touched upon: who has the time/sadomasochistic inclination to fully subject themselves to over 30 posts from the Discovery Institute? Not I, not I.

Orca eats shark

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I think this story calls for revising the rules of Rock-Paper-Scissors-Lizard-Spock into Rock-Paper-Scissors-Orca-Shark. You know, Paper covers Rock, Scissors cut Paper, Orca puts Shark into state of tonic immobility.

ResearchBlogging.org In the cartoon version of evolution that is often employed by critics of the theory, a new protein (B) can arise from an ancestral version (A) by stepwise evolution only if each of the intermediates between A and B are functional in some way (or at least not harmful). This sounds reasonable enough, and it’s a good starting point for basic evolutionary reasoning.

But that simple version can lead one to believe that only those mutations that help a protein, or leave it mostly the same, can be proposed as intermediates in some postulated evolutionary trajectory. There are several reasons why that is a misleading simplification - there are in fact many ways in which a mutant gene or protein that seems to be partially disabled might nevertheless persist in a population or lineage. Here are two possibilities:

1. The partially disabled protein might be beneficial precisely because it’s partially disabled. In other words, sometimes it can be valuable to turn down a protein’s function.

2. The effects of the disabling mutations might be masked, partially or completely, by other mutations in the protein or its functional partners. In other words, some mutations can be crippling in one setting but not in another.

In work just published by Joe Thornton’s lab at the University of Oregon, reconstruction of the likely evolutionary trajectory of a protein family (i.e., the steps that were probably followed during an evolutionary change) points to both of those explanations, and illustrates the increasing power of experimental analyses in molecular evolution.

A reader sent me this link with the subject line above. The state and the county have committed $40 million in tax credits, as well as other perks, to a for-profit venture to build an Ark Park in order to spur “economic development.” Someone may correct me, but unless I am mistaken such enticements for sports stadiums and other ventures almost never pay for themselves. Besides, a state senator notes at the bottom of the article, the developer said it did not need the incentives, so why were they offered?

See also an earlier article here.

Gene patenting upheld

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About two weeks ago, the Federal Circuit–one of the nation’s Courts of Appeals, and therefore the second-highest level of the federal judiciary–handed down its decision in Association for Molecular Pathology v. PTO, a case about the controversial subject of gene patenting. The court upheld the patenting of genes–though not other patents, which cover certain methods of comparing or testing genes, and this has sparked some (to my mind, correct) outrage on the part of researchers, who see gene patenting as an obstacle to research and progress in genetics. Because this is not really about evolution, I examine the decision over at my personal blog, Freespace.

Rainbow

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Photograph by Wayne Robinson.

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Rainbow, off Lion Rock, Galápagos Islands, June, 2009.

[Review of Shapiro, James A. Evolution: A View from the 21st Century. FT Press Science, ISBN: 0-13-278093-3, $34.99 Publisher’s site]

Over the years there have been many books that purport to “radically revise” or “supplant” Darwinian evolutionary biology; they come with predictable regularity. Usually they are of three kinds: something is wrong with natural selection, something is wrong with inheritance, or something is wrong with phylogeny. This book, by geneticist James A. Shapiro, exemplifies all three.

Did God create the universe?

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According to an advance review of a program tonight on the Discovery Channel, Stephen Hawking (unsurprisingly) says no. In the U. S., the program is on the tube at 8:00 Eastern time.

Springboro Update

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Kelly Kohls, the nutritionist and school board member in Springboro, Ohio, who advocated teaching creationism in that district, has revised her position. She now says that she

…wants parents of students in public schools to have options if they want their children to learn about theories like intelligent design.

and that

… parents should have the choice of using state funds to send their children to other schools if they want to learn about creationism and intelligent design.

A potential route, she thinks, is school vouchers, where state money is paid to parents to send their children to private, often sectarian, schools.

Read more in the Dayton Daily News. One parent quoted there has exactly the right idea:

Tina Gangl, who has a daughter in Springboro elementary school and a son at the nearby Catholic Bishop Fenwick High School, said public schools should not teach religion.

“We need to educate our children about science,” Gangl said, “If I want to teach my religion to my kids I’ll send them to a religious school. There is no place for it in public school.”

ResearchBlogging.org“The Selfish Gene.” “Selfish DNA.” Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda’s Thumb), and Richard Dawkins devoted more time to answering critics of his use of the term ‘selfish’ than should have been necessary. Dawkins’ thesis was pretty straightforward, and he provided real examples of “selfish” behavior of genes in both The Selfish Gene and its superior sequel, The Extended Phenotype. But there have always been critics who can’t abide the notion of a gene behaving badly.

Leaving aside silly bickering about the attribution of selfishness or moral competence to little pieces of DNA, let’s consider what we might mean if we tried to imagine a really selfish piece of DNA. I mean a completely self-centered, utterly narcissistic little piece of DNA, one that not only seeks its own interest but does so with rampant disregard for other pieces of DNA and even for the organism in which it travels. Can we imagine, for example, a piece of DNA that deliberately harms its host in order to propagate itself?

by Joe Felsenstein

http://evolution.gs.washington.edu/felsenstein.html

Not only was he one of the most interesting evolutionary biologists, he was really the first major biologist to not only say that evolution happened, but to provide a mechanism to explain adaptation (albeit a wrong mechanism). He was born on August 1, 1744 in Bazentin-le-Petit, France. So if he had lived, he would be 267 years old today. He coined the term “invertebrate” (because he did brilliant work on them), and, for that matter, he coined the term “biology”! He did not invent “Lamarckian inheritance”, he just used it in his evolutionary mechanism – everyone back then already believed in it.

So happy birthday, Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck! here and here are my previous birthday postings for him, with interesting discussion over such issues as whether his evolutionary tree can really be regarded as an historical genealogy.

Another year, another clueless school board

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Springboro, Ohio, described by Wikipedia as “an affluent suburb of Cincinnati and Dayton,” has a school board on which two members are pushing for the inclusion of creationism in the district’s science curriculum. The Dayton Daily News reported today that BOE members Kelly Kohls and Scott Anderson, elected on a platform of fiscal responsibility, are one vote away from a creationist majority on the Board. According to the story, Kohls requested that

… the district’s curriculum director look into ways of providing “supplemental” instruction dealing with creationism.

It goes on

“Creationism is a significant part of the history of this country,” Kohls said. “It is an absolutely valid theory and to omit it means we are omitting part of the history of this country.”

Consistent with Lenny Flank’s law, though, Kohls makes the motivation for her advocacy of creationism clear:

Kohls is the head of the Warren County Tea Party. Although she said her desire to teach creationism is not directly related to the emerging political movement, it’s not inconsistent with Tea Party ideals.

“My input on creationism has everything with me being a parent and not a member of the Tea Party,” she said. “We are motivated people who want to change the course of this country. Eliminating God from our public lives I think is a mistake and is why we have gone in the direction of spending beyond our means.”

Nice.

There’s some support for the push from another source:

John Silvius, a former biology professor at Cedarville University, a Christian institution that teaches both evolution and creationism, said the two theories can co-exist, even in a public school classroom.

Cedarville is a Baptist young-earth institution; it even has a young earth geology program, taught, it is claimed, from “both naturalistic and young-earth paradigms of earth history.”

I trust that the curriculum director will read documents like Edwards v. Aguilar, McLean v. Arkansas, and Epperson v. Arkansas, not to mention Kiztmiller v. Dover. I also hope that the Board’s legal advisers have their wits about them.

The two creationism-pushing board members were supposedly elected on a fiscal responsibility platform. How fiscally responsible is it to expose the district to expenses in the hundreds of thousands of dollars by advocating a bankrupt religious approach in public schools? The Mt. Vernon, OH, and Dover, PA, boards could provide Springboro with some advice on just how “fiscally responsible” pushing creationism is. The same sort of shenanigans cost those districts on the order of $1m each.

It is of course a cliche to state that eukaryotic cells (i.e., cells that are not bacteria) are complex. In the case of an animal, tens of thousands of proteins engage in fantastically elaborate interactions that somehow coax a single cell into generating a unique and magnificent organism. These interactions are often protrayed as exquisitely precise, using metaphorical images such as ‘lock-and-key’ and employing diagrams that resemble subway maps.

Many of these interacting proteins are enzymes that modify other proteins, and many of those enzymes are of a particular type called kinases. Kinases do just one thing: they attach phosphate groups to other molecules. This kind of modification is centrally important in cell biology, and one way to tell is to look at how many kinases there are: the human genome contains about 500 kinase genes.

Now, kinases tend to be pretty picky about who they stick phosphate onto, and this specificity is known to involve the business end of the kinase, called the active site. The active site is (generally) the part of the kinase that physically interacts with the target and transfers the phosphate. You might think that this interaction, between kinase and target, through the active site, would be by far the most important factor in determining the specificity of kinase function. But that’s probably not the case.

Carnival of Evolution 38

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CoEButton.jpgThe 38th Edition of the Carnival of Evolution is now open for business at Sandwalk.

It is massive and magnificent. Bats, bears, bugs. “The science of sexism” and “How to save your marriage.” Using deleterious mutations to cross fitness valleys. Cryptozoology. And, of course, a nice list of recommended iPhone apps.

Get comfortable and enjoy this epic edition of the carnival.

Crotalus adamanteus

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Crotalus adamanteus – eastern diamondback rattlesnake, preserved in the Vertebrate Natural History collection at University of North Carolina at Wilmington. Mr. Shackleton writes, Sadly, the interesting and differentiating colors of preserved specimens rarely lasts long in the alcohol. A lot of undergraduate pain and suffering would be relieved if someone came up with a preservative that didn’t suck all the life out of the specimens (the alcohol bleeds all the color out of the specimens, and makes it a real pain to identify them). You may see more of Mr. Shackleton’s photographs here.

A reader, Dan Phelps, tells me, “Looks like the ‘fiscal conservative’ school board member is going to cost his district a lot of money.” See here, and stay tuned to a local newspaper near you.

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