February 2008 Archives

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)

Essay Contest— get those submissions in!!!

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.

ReMine Strikes 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.”

Darwin Day in Kentucky


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.


Expelled with the Banned


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.


Let the party begin.

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.

Your Inner Fish - Hiccups


inner fish.jpgNeil 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.


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.

Luskin conflating design inferences


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)

Tangled Bank #99

The Tangled Bank

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.

Read the rest at Freespace…

Comments may be left in our forum.

Plant and animal development compared

Blogging on Peer-Reviewed Research

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:

Some good news from Florida


pandathumbla7.jpg 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

Happy Darwin Day!


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.

Well that didn’t take long


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:

From the Iowa State Daily:

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…

Some good news from Florida


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 Sch�tzenberger (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.

The double edge sword


Dembski, somewhat ironically, quotes from January 13th 2008 - Sheldrake exposes Dawkins as a fundamentalist pseudoskeptic which references a blog article by Rupert Sheldrake

Dawkins has of course every right to promote his religious views- in this case, the religious views of atheistic materialism, which considers evidence for presumably transcendental phenomena a mortal threat to its belief system.However, when Dawkins and people like him promote their views in the name of science, they commit labeling fraud. Dawkins may be a scientist by trade, but when he acts and argues as a fundamentalist believer in materialism, ignoring evidence that challenges his belief system, then he commands no more credibility and scientific authority than any other kind of religious believer.

I could not agree more… If Dawkins were to be promoting his (religious) views in the name of science then they are as guilty of labeling fraud and he commands no more credibility and scientific authority than any other kind of religious believer.

I doubt if Dembski appreciated the double edge sword.

Good signage at Tangled Bank #98

A baffling failure of peer review


A dismaying update: the paper in question contains a significant amount of outright plagiarism, and large chunks of text are taken literally from Butterfield et al. 2006, “Oxidative stress in Alzheimer’s disease brain: New insights from redox proteomics,” European Journal of Pharmacology 545: 39-50. I hope we hear from Han and Warda sometime; they've got a lot of 'splaining to do.

Mitochondria are fascinating organelles. They are the "powerhouses of the cell" (that phrase is required to be used in any discussion of their function) that generate small, energy rich molecules like ATP that are used in many cellular chemical reactions, but they also have important roles in cell signaling and cell death. They also have a peculiar evolutionary history, arising as endosymbionts; their ancestors were independent organisms that took up residence inside eukaryotic cells in a mutually happy and long-lasting relationship. They exhibit some interesting relics of that prior history, as mitochondria have their own private strand of DNA which encodes some of the genes needed for the chemical processes they execute. Other genes for those functions have migrated over evolutionary time into the nuclear genome, which means the mix of gene products operating in the organelle are from two sources, the mitochondrial and nuclear genome. It's a good subject for studies in proteomics.

Right now, there is a paper that is available as an Epub ahead of print in the journal Proteomics. It is not promising. In fact, all you have to do is read the title to make you wonder what the authors, Warda and Han, were smoking: "Mitochondria, the missing link between body and soul: Proteomic prospective evidence."

Attila Csordas asks, "Can you tell a good article from a bad based on the abstract and the title alone?", and I'm inclined to say yes. Sometimes you get pleasant surprises in the full paper that were not well described in the abstract, but when the abstract and title contain hints that the bridge is out and that somebody has switched the train to the wrong tracks, you can predict that there will be a train wreck if you read further. Here's the abstract. I've highlighted one provocative statement.

Mitochondria are the gatekeepers of the life and death of most cells that regulate signaling, metabolism, and energy production needed for cellular function. Therefore, unraveling of the genuine mitochondrial proteome, as the dynamic determinant of structural-functional integrity to the cellular framework, affords a better understanding of many still-hidden secrets of life behind the already known static genome. Given the critical mitochondrial role under different stress conditions, the aim of the current review is to merge the available scientific data related to mitochondrial proteomes and frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader fundamental mechanisms orchestrating cellular outcome on behalf of cell survival. The focus of this work is to cover first the mitochondrial proteome/genome interplay that is currently believed to be implicated in a range of human diseases. The mechanochemical coupling between mitochondria and different cytoskeleton proteins and the impact of the mitoskeleton on mitochondrial structure and function are then addressed. Further crosstalk between mitochondria and other cellular organelles, e.g., the ER and the nucleus is then discussed. Additionally, the role of mitochondria in apoptosis and the mitochondrial contribution in intercellular communication mediated by gap junctions are also described. These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative. Furthermore, the role of mitochondria in development of oxidative stress-based diseases, e.g., neurodegenerative and cardiovascular diseases is pointed out together with the prospective proteomics view as an alternative prognostic and diagnostic tool for interpreting many mitochondria-related anomalies. The insights generated by recent proteomic research that provide a rational impact on possible mitochondrial-targeted therapeutic interventions are also discussed.

My blog makes a career out of describing train wrecks, so how could I not continue on and read the paper?

Continue reading "A baffling failure of peer review" (on Pharyngula)

Loss of a giant: Joshua Lederberg


Joshua Lederberg passed away on Saturday.

Joshua Lederberg, Nobel Prize-winning molecular biologist who shaped the field of bacterial genetics, and served as chair of The Scientist’s advisory board since 1986, died on Saturday (February 2). He was 82.

Lederberg shared a Nobel Prize in physiology and medicine in 1958 for the discovery that certain strains of bacteria reproduce by mating, thereby exchanging their genetic material. This overturned the idea held at the time that bacteria did not warrant genetic study and set the field of bacterial genetics into motion.

Lederberg truly was a visionary, and along with his ex-wife, Esther (who died just over a year ago), really jump-started the field of microbial genetics (and indeed, made it much easier to study genetics, period), winning a Nobel prize for his genetic work when he was only 33. Years later, he teamed up with Carl Sagan to raise awareness about microbes in space, and was an advocate of science communication and sound policy (serving as an advisor for multiple presidents). In recent years, he’s spoken out about antibiotic resistance and bioterrorism, among other topics, and always emphasized the importance of basic research in microbiology. He could also give a helluva interesting talk, judging from the few times I’ve seen him speak. He was truly a living legend, and the void he leaves is palpable.

More info and access to papers at the here at the National Library of Medicine. Image from here.

Yesterday, I wrote a post about Casey Luskin’s misuse of the ResearchBlogging.org “Blogging about Peer-Reviewed Research” icon. Today, Casey removed the icon from his post, and provided an explanation for his actions. I’m glad that he decided to cease his misuse of the icon, but his explanation leaves a heck of a lot to be desired. He admits no wrongdoing, makes no apology, and presents a series of excuses for his actions that - even if accepted at face value - are weak at best.

The first excuse he presents is essentially a claim that he didn’t know what he was doing:

A co-worker had recommended that I include a graphic that said this was discussing peer-reviewed research. At the time, I was unaware of ResearchBlogging.org and the fact that they requested registration in order to use their graphic. Important note: It should be clear that when I first posted my post, I had not yet seen ResearchBlogging.org and was unaware of how it worked. (Italics in original.)

I’m finding it very hard to believe that Casey was unaware of ResearchBlogging.org when he used the icon. Here’s why:

Read more at The Questionable Authority, where comments may be left:

Casey Luskin has a post up over at the Discovery Institute’s website that discusses an article that was recently published in PLoS Biology. The post itself is nothing particularly remarkable - Casey takes a paper that says that current hypotheses don’t adequately deal with all of the problems of figuring out how life started, and claims that a lack of a workable hypothesis is evidence that an Intelligent Designer is needed to explain how life got here. Along the way to the argument from ignorance, he manages to misrepresent portions of the article, put words into the author’s mouth, and use three little dots to chain sentences located paragraphs apart into a single quote. In most respects, it’s a fairly typical example of Discovery Institute work.

This time, though, Casey added a little something extra to his usual work product. He stuck a little image up at the top left corner of his post. His use of the icon in question demonstrates an eagerness to assume the trappings of intellectual respectability without actually making the effort to be respectable.

The icon in question is the ResearchBlogging.org “Blogging About Peer-Reviewed Research” icon. You may have seen the icon before. I’m one of a large (and growing) number of bloggers who have used the icon to mark posts that feature an in-depth discussion of an article found in the peer-reviewed literature. The ResearchBlogging.org website provides a single location where you can find all of the properly marked posts.

Read more at The Questionable Authority, where comments may be left:

Aaron Elias, sophomore student in English, writes in the New University (University of California of Irvine) the following:

Every so often, a group will try to promote its cause and give itself the proverbial rake in the face. The pointy end of the rake came up when the makers of “Expelled: No Intelligence Allowed” started bribing fundamentalist schools to organize mandatory field trips forcing students to watch the film. Bribery? Great publicity move! That garners about as much credibility as a Republican politician in a bathroom stall.

and that’s not all…

Dembski: Expelled, the true reason

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In an article by the Southern Baptist Texan, Dembski describes why people should be watching ‘Expelled’. And no it is not because of the suppression of the ‘science’ of intelligent design, no, no no. It’s all about the idea that there is a “…Darwinian, atheistic mafia whose purpose is to ruin the careers of anybody who delves into the idea of intelligent design.”

Not surprisingly he argues (sic) that:

Dembski Wrote:

Dembski told the Southern Baptist TEXAN that those who most need to see the movie are “parents of children in high school or college, as well as those children themselves, who may think that the biological sciences are a dispassionate search for truth about life but many of whose practitioners see biology, especially evolutionary biology, as an ideological weapon to destroy faith in God.”

St Augustine explained it well when he stated:

Well, the Intelligent design Challenge is over, and we have a winner(s). It was interesting looking at the various methods people used, and I’ll discuss this below the fold. One thing stood out though.

No one used the explanatory filter, or any of the various methods proposed by Intelligent Design proponents. Not one person.

The Orlando Sentinel has an article by Roger describing the pre-screening of Ben Stein’s movie ‘Expelled’

How do you re-package that tried, untested and untestable faith-without-facts warhorse, “Creationism” after its nearly-annual beat-down by an increasingly exasperated scientific community?

After you’ve tried renaming it “Intelligent Design,” I mean.

With comedy. Mock your “Darwinist” foes the way comics, thinkers, scientists and educated people everywhere have been mocking creationism since Scopes took that monkey off our back.

Our friends at Florida Citizens for Science have launched an online petition to keep the pressure on the state Board of Education to adopt the new proposed science standards as they are and not water them down with creationist nonsense. We urge you all to sign it, especially if you are from Florida.

In my observations that Intelligent Design is scientifically vacuous I have pointed out how ID proponents have failed to present any non-trivial Design Inference where the ID approach actually worked. However, history is full of false positives, even though ID proponents such as Dembski are adamant that false positives do not occur since this would render the filter useless. And for good reason because this would mean that ID’s design inference cannot compete with our ignorance.

In a recent posting on Uncommon Descent, ID proponents showed their disappointment with Discovery Institute’s Senior Fellow Simmons performance in his much touted debate (click to download MP3 file) with PZ Myers. Soon thereafter, the link was deleted, showing how Intelligent Design is not truly interested in teaching the controversies, when said controversies make ID look foolish.

Luckily the comments were saved by antievolution.org

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