Monday's Molecule #224

Last week's molecule was the second messenger, phosphatidylinositol 4,5-bisphosphate or PIP₂. The winner is Dean Bruce. The undergraduate winner is Ariel Gershon [Monday's Molecule #223].

Today's molecule is a protein (purple). It's one of the most abundant proteins in E. coli because it's bound to almost all tRNA molecules in the cell. Name the protein (complete name, not just initials).

Email your answer to me at: Monday's Molecule #224. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

What is bioethics? Is Margaret Somerville a bioethicist or a Roman Catholic apologist?

I had an interesting conversation with a student the other day. She's studying "bioethics" at the University of Toronto. This is a program run by the Deptment of Philosophy.

I asked her to define "bioethics" and she couldn't. To her credit, she immediately recognized that this wasn't right. If she's taking an entire program in bioethics she ought to be able to explain what it was all about. She was then joined by her friend, who is also majoring in bioethics. My colleague, Chris DiCarlo also joined us. He's a philosopher writing a book on ethics.

We described a scenario where I wanted to end my life and Chris was willing to help me. Neither of us have an "ethical" problem with that decision. So why is assisted suicide thought to be a problem for bioethics? If some people don't want to participate in euthanasia then nobody is going to make them? Where's the problem?

Does it only become a bioethical problem if some people want to impose their views on others? In this case, the people who are personally opposed to euthansia want to pass a law preventing me from ending my life with the help of my friend. Our students were puzzled by this discussion. Even though they have taken many courses on bioethics, nobody had ever raised this issue. Isn't that strange? You would think that any program run by a Department of Philosophy would emphasize critical thinking. Sadly, this turns out to be rare whenever the topic of bioethics comes up.

You simply won't believe what the IDiots are saying now!

Do you remember Vincent Joseph Torley (vjtorley)? He's the IDiot with a Ph.D. (2007) from the Department of Philosophy at the University of Melbourne (Australia). That's a legitimate university. Apparently Vincent Torley went off the rails sometime after 2007.

Here's his latest post on Uncommon Descent: Does scientific knowledge presuppose God? A reply to Carroll, Coyne, Dawkins and Loftus.

The scientific enterprise stands or falls on the legitimacy of making inductive inferences, from cases of which we have experience to cases of which we have no experience. The aim of this post will be to show that there can be no scientific knowledge if there is no God, and that there is no way of justifying inductive inference on a systematic basis, in the absence of God.

BLAH, BLAH, BLAH, etc. etc. etc.

I alluded above to the troubling fact that even if we assume that objects somehow instantiate rules, there remains the epistemic problem of knowing whether we’ve chosen the right model, or identified the right mathematical equation (i.e. laws of Nature) for characterizing the rules that define a certain kind of object – be it a tiny electron or a star, like the sun. But if we make the two assumptions about God which I referred to in the preceding section – that God wants to make intelligent beings, and that God wants these intelligent beings to reason their way to God’s existence – then we can infer that the rules which are embodied by objects in the natural world must be tailor-made to fit the minds of intelligent beings that are capable of contemplating their Creator. In other words, the universe is designed to be knowable by us. Hence we don’t need to concern ourselves with the theoretical possibility that the rules which characterize things might be too complicated even in principle for us to grasp.

God, then, is the ultimate Guarantor that science can work.

Well, that does it for me. Either I stop being a scientist or I have to become a believer in God in order to continue doing science.

Tough choice. Let me get back to you on that one ... anyone want a job as a professor of biochemistry?

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God Only Knows by The Beach Boys

The Pet Sounds album by The Beach Boys was released in 1966. The album ranks in the top ten of almost everyone's list of best albums (English/American culture). It's #2 on Rolling Stone's list of the 500 Greatest Albums of All Tine.

I wasn't a big fan of the album but I adored God only knows, and I still do.¹ It's one of my top ten favorite songs. The song ranks at #25 in Rolling Stone's 500 Greatest Songs of All Time. Paul McCartney, who played for another popular group in the 1960s, says that God Only Knows is his favorite song of all time.

The music was written by Brian Wilson² and the lyrics are by Tony Asher. I don't know very much about music so you'll have to read the Wikipedia article to appreciate why so many people admire Brian Wilson. Carl Wilson, Brian's younger brother, sings the song.

The video is from Good Timin': Live at Knebworth England 1980. It's one of the rare occasions after 1965 when all six Beach Boys (Brian Wilson, Dennis Wilson, Carl Wilson, Mike Love, Al Jardine and Bruce Johnston) are together. I think it's the only video where Brian Wilson is playing on God Only Knows. (That's him on the piano.)

I never saw a live performance of the original Beach Boys but I've seen the Mike Love version twice.

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1. Some atheists will never like this song because it mentions God. That sort of thing doesn't bother me. I can still sing God Save the Queen and the Canadian national anthem without batting an eyelash. There are much more important things to fret about.

2. I just read in the Wikipedia article that he was inspired by the Lovin' Spoonful song You Didn't Have to Be So Nice. That song is also one of my personal favorites but I never twigged to the similarity until now.

Little Richie Dawkins

One thing that draws me to the ID movement is that it has the polite and understated ethic that science is supposed to have -- but does not have when the subject is evolution.

Stephen A. BatzerHere's a video that was posted today on Uncommon Descent by Salvador Cordova. Before watching it, read my post on: Why are Darwinists do uncivil?. It links to an IDiot post by Stephen A. Batzer where he complains about "Darwinists" being uncivil.

Here's one of the points that Batzer makes ...

Thought leaders in the Darwinian movement, such as Dawkins, Prothero, Shermer and so on, inculcate and advocate incivility by their own example. Look at the way biologist James Shapiro and philosopher Jerry Fodor have been treated. It's ugly.

The video was produced by Mike Booth. Decide for yourself if the evolution side of the debate behaves like the IDiots. (Apologies to Richard Dawkins for propagating this nonsense but people need to see the depths to which the Intelligent Design Community can sink.)


UPDATE: Denyse O'Leary has responded to this post [Huh? Actually, we thought Little Richie (Dawkins) was a special creation, just for us…]. She says, "Moran thinks it originated in the ID community. Unclear why because it’s really not about our usual questions and concerns." Actually I don't know anything about Mike Booth or whether he is a support of Intelligent Design Creationism. I looked, but I couldn't find anything. What I do know is that IDiots like Denyse O'Leary post the obnoxious video on their websites. O'Learly also says this about the video, "It’s also not a lot nastier than the old showman himself." I think I'll let intelligent people decide for themselves who is nastier. I'm glad that Denyse O'Leary at least acknowledges that the video she posted was nasty.

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Unchained Melody by The Rightous Brothers

Is it true that the music of the Baby Boomers is a whole lot better than the music of Generation-X or the Millennials (Generation-Y)? Of course it's true. Those whippernappers couldn't touch the best music of the 1960s.

Here's a song that makes my top ten list, although I will admit that it's only #374 on 500 Greatest Songs of All Time. I'm pretty sure this must be a mistake. Rolling Stone also seems to have made a mistake with #9.


(For some strange reason, my son and daughter don't seem to appreciate the music of my generation. I don't know where I went wrong.)

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A new definition of kindness and empathy? (on educating children)

Today's version of the Toronto Star has several articles on kindness and empathy. The feature article appears on the front page of the "Insight" section. The title of the print version is "Kindness: A fledgling movement aims to instil empathy and make us a kinder, gentler, society." The online version is How to fight meanness? Try a bit of kind.¹

The article is written by education reporter Louise Brown. The gist of the article is that we need to teach empathy and kindness² and perhaps the schools should be involved. But the main teachers should be parents.

Denyse O'Leary is at it again! (re: junk DNA)

In Denyse O'Leary's latest post she claims (again) that "Darwin's followers" used junk DNA as an argument for their position [What? Darwin’s followers did not use junk DNA as an argument for their position?].

No, Denyse, "Darwin's followers" (i.e. adaptationists) never used the presence of large amounts of junk DNA as evidence of the power of natural selection. Such a position would be absurd. The vast majority of "Darwin's followers" were opposed to the idea of large amounts of junk in a genome. Many still are.

Read this post and the links it contains: Darwinists Don't Believe in Junk DNA. You might enjoy my critique of Jonathan Wells book. (You can read, can't you?)

Denyse, you and the other IDiots are confused about a lot of things but this particular debate seems to have you all completely flummoxed. None of you seem to be capable of listening or of understanding simple logic.

It's true that many supporters of evolution evolutionary biologists like Francis Collins, Richard Dawkins, and Ken Miller used the presence of similar pseudogenes in different species as powerful evidence for common descent. They also pointed out that IDiots have a hard time explaining such pseudogenes. A direct challenge, by the way, that IDiots have avoided.

It's true that pseudogenes are junk. That does not mean that Collins, Dawkins, and Miller believe that most of our genome is junk. They are not saying that because most of our genome is junk, evolution must be true.

Denyse doesn't buy this when a commenter on her blog tried to explain it. She asks,

Question for readers here: Is it a sign of weakness in the Darwinians’ position that they can’t acknowledge that they made mistakes? They seem to have to defend, then deny.

Oops! Did I forget to tell you to turn off your irony meters? Sorry.

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Those who cannot remember the past are condemned to repeat it

• November 22, 1963: President John F. Kennedy was assassinated.
• April 4, 1968: Martin Luther King Jr. was assassinated.
• June 6, 1968: Robert F. Kennedy was assassinated.
• July 21, 1969: Neil Armstrong walks on the moon.

You tell me that I need to forget these events as though they never happened?

You tell me that you don't care because you weren't born yet?

This post was prompted by something that Andrea Habura wrote on Facebook. She says that she is an "R&D Scientist at Next Advance, Inc." Here's what she wrote ...

The demographics of Camelot: As you will no doubt have heard by now, today is the 50th anniversary of the Kennedy assassination. I've also been repeatedly informed that everyone is still shocked and saddened by it, and that "we" will never forget how we felt when we heard the news.

Dear newscasters: Most Americans were either not alive yet, or too young to notice. Only 25% of Americans are over 55 (http://www.indexmundi.com/united_states/demographics_profile.html), and some of them were living in other countries in 1963. To most of us, the shooting in Dallas was about like what happened in Ford's Theater, with the exception that our teachers seemed to feel *really* strongly about it. Let it go.

Just for the record, I understand how my parents felt on May 5, 1945 (VE Day) even though I wasn't born yet. I understand how they felt when Hiroshima and Nagasaki were destroyed by atomic bombs. I think I know how they felt on March 29, 1945 when President Roosevelt died.

I understand what my parents and my grandparents went through on October 29, 1929 when the stock market crashed and life's saving were lost. I listened when they told me of the pain and suffering during the great depression. I never told them to "let it go."

I'd like to think I know how traumatic it must have been for Americans on April 15, 1865 even though I wasn't there.

Dear Andrea,

The world did not begin when you were born. Listen and learn from your elders. You will be a better person.

Those who cannot remember the past are condemned to repeat it.
                                                                        George Santayana

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On a Friday Afternoon 50 Years Ago

It was about 3pm and I was sitting in my geometry class at Nepean High School in Ottawa, Canada. This was my final year of high school. I liked this course and I liked my teacher (Mr. Pollack).

The loudspeaker crackled and I heard the Principle's voice. Mr. Callan said that President Kennedy had been shot and killed in Dallas.

Kennedy was not my President but it was still a great shock. It seemed like Camelot had been destroyed.¹ I spent the next three days in front of the television set. Nobody knew what was going to happen to America.

You know how everyone says they know exactly where they were and what they were doing when major events happen? That's certainly true for me on the day John F. Kennedy was assassinated. It's one of only two days in my life that I remember so vividly.² If it was traumatic for a young Canadian boy, I can't imagine what it must have felt like for Americans.

How many of you remember Nov. 22, 1963?

It looks very naive now but back in 1963 we really believed that Camelot and King Arthur could be real. Here's Richard Burton in the Broadway production. It seems like everybody had the album.

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1. The musical, Camelot had been playing on Broadway since 1960 and everyone was familiar with the music from the LP (record album). The Kennedy family and the Kennedy administration were intimately associated with the idea of Camelot.

2. The other was Sept. 11, 2001.

What Could Possibly Be Wrong with Putting a Cute Dog on the Cover of Science?

Nothing could be wrong until you realize that Science writer editor Elizabeth ("Liz") Pennisi is behind it. That changes things entirely.

To find out why you have to read Dan Graur's latest at: A Dog on the Cover of @ScienceMagazine: Sins of Omissions.

At some point, the big bosses at Science magazine are going to have to wake up to the fact that they're publishing a lot of bad papers and commentaries. Something is seriously wrong.

David Klinhoffer likes Elizabeth Pennisi: Shooting the Messenger: Elizabeth Pennisi. He says ...

As we frequently hasten to emphasize about daring writers and researchers in science, I have no reason to think Pennisi is a Darwin skeptic much less a proponent of ID. Still, she's a reporter who is open to promoting "evolution heresy." She's unafraid to challenge the old guard. More than once she has stuck her finger in the eye of ancient régime. Now you know why she ticks off guys like Graur and Moran.

Yep. He got that right. Graur and I are definitely part of the old regime and we don't like people who promote evolution heresy ... or their sycophants.

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Claudiu Bandea Shows Why Attacking Dan Graur Is a Very Bad Idea

Claudiu Bandea is a frequent commenter on this blog. Whenever the subject of junk DNA comes up he reminds us that he had a theory over twenty years ago. Now he has published(?) an advertisement at: On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al.. Here's the abstract ...

In a recent article entitled “On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE”, Graur et al. dismantle ENCODE’s evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNA’s biological functions to informational roles, sidestepping putative non-informational functions. Here, I bring forward an old hypothesis on the evolution of genome size and on the role of so called ‘junk DNA’ (jDNA), which might explain C-value enigma. According to this hypothesis, the jDNA functions as a defense mechanism against insertion mutagenesis by endogenous and exogenous inserting elements such as retroviruses, thereby protecting informational DNA sequences from inactivation or alteration of their expression. Notably, this model couples the mechanisms and the selective forces responsible for the origin of jDNA with its putative protective biological function, which represents a classic case of ‘fighting fire with fire.’ One of the key tenets of this theory is that in humans and many other species, jDNAs serves as a protective mechanism against insertional oncogenic transformation. As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size.

It's not a good idea to attack someone who; (a) is an expert in the field, (b) is intelligent and outspoken, and (c) has a blog. But that never stopped Claudiu Bandea before so why should it now?

Here's part of how Dan Graur responds at: A Pre-Refuted Hypothesis on the Subject of “Junk DNA”. There's more, read it all.

The first problem with this hypothesis is that big eukaryotic genomes consist mostly of very few active transposable elements and numerous dead transposable elements. So, big genomes seem to need little protection. Moreover, a positive correlation exists between genome size and number of transposable elements. In 2002, Margaret Kidwell published a paper entitled “Transposable elements and the evolution of genome size in eukaryotes.” In it, she showed that an approximately linear relationship exists between total transposable element DNA and genome size. Copy numbers per family of transposable elements were found to be low and globally constrained in small genomes, but to vary widely in large genomes. Thus, the major characteristic of large genomes is the absence of selective constraint on transposable element copy number.

Given that the vast majority of transposable elements are dead, the most parsimonious explanation is that the continuous accumulation of dead transposable elements is the reason for genomes becoming large. Let me spell it out: the “large” part in “large genomes” is made of transposable elements. Genome do not become large first and then protect genetic information by becoming sinks of transposable elements.

The other problem with the protection-from-mutation hypothesis is that it assumes selection on mutation to be effective. Selection on mutation is referred to in population genetics as second-order selection. The reason is that this type of selection is anticipatory. It protects against a possibility, not an actuality. Second-order selection on mutation (mutability) requires huge effective population sizes, so huge in fact that they are only found in a few bacteria and viruses. Unfortunately for the protection-from-mutation hypothesis, genome size is known to be inversely correlated with effective population size. In other words, huge genomes are found in species that have very small effective population sizes. So small, in fact, that even regular selection (first-order selection) is not very effective.

Thomas Huxley was proven right again: "The great tragedy of Science is the slaying of a beautiful hypothesis by an ugly fact." Several ugly facts in this case.

I can't count the number of people who have tried to explain to Claudiu Bandea that his idea is ridiculous. Hopefully, this last embarrassment will silence him.

Naturally, the Intelligent Design Creationists are all over it [Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings].

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Which Way Did Darwin Walk?

For some reason the title reminds me of "What Does the Fox Say." Oh well, PZ Myers is desperately interested in knowing which way Darwin walked when he took a stroll on the Sandwalk [An important historical question!].

I know which way PZ walked 'cause I led him!

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Sylvia Browne Blows Another Psychic Prediction

I first became aware of Syvlia Brown when I saw her on Larry King Live ten years ago [Interview with Sylvia Browne]. As most of you know, Larry King is a real sucker for quacks of all types and he used to let psychics like Sylvia Browne respond to listeners who called in to the show. It was always good for a laugh.

In the middle of that part of the show we have this exchange.

KING: OK. Do you know when you're going to die?

BROWNE: Yes. When I'm 88.

Later on I was happy to post a link to Anderson Cooper's debunking of Sylvia Browne on CNN [Psychic Sylvia Browne Is Nothing but a Con Artist and a Fake].

Sylvia Browne died yesterday [Psychic Sylvia Browne, famous for TV appearances, dies at 77]. She was 77 years old. Only off by 11 years.

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[Hat Tip: PZ Myers: Didn’t see that one coming]

Is Baker's Yeast a Good Model for the Evolution of Multicellularity?

R. Ford Denison has an excellent blog called This Week in Evolution. He recently posted an article about the evolution of multicellularity [Evolving-multicellularity lab exercises]. That post contains a link to a paper he recently published with a former student (Ratcliff et al., 2013). Here's the abstract.

Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood. Using experimental evolution, we show that key steps in this transition could have occurred quickly. We subjected the unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to be adaptive. We observed the rapid evolution of clustering genotypes that display a novel multicellular life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest. Simple among-cell division of labor rapidly evolved. Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production. These results show that key aspects of multicellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes.

Here's the problem. Most fungi are multicellular and Saccharomyces cerevisiae (budding yeast) almost certainly evolved from an ancestor that could form hyphae. In fact, wild-type diploid strains or Saccharomyces cerevisiae will form multicellular filaments (pseudohypha) in response to starvation for nitrogen (Liu et al., 1996).

Many of the common lab strains have lost the ability to form multicellular pseudohyphae because they carry a nonsense mutation in the FLO8 gene (Liu et al., 1996). Presumably, those strains have been selected by bakers and brewers over the past several thousand years.

In their discussion, Ratcliff et al. (2012) say ...

Although known transitions to complex multicellularity, with clearly differentiated cell types, occurred over millions of years, we have shown that the first crucial steps in the transition from unicellularity to multicellularity can evolve remarkably quickly under appropriate selective conditions.

I don't this this is quite fair since the yeast strain is just reverting to a primitive condition. This might only have required one or a few mutations. It's not a very good model for de novo evolution of multicellarity.

The work from Gerry Fink's lab (e.g. Liu et al. 1996) is a good example of why we should be cautious using yeast as a model for anything. The yeast strains used in the lab have been selected for specific characteristics since bread-making and beer-making were first invented over 4000 years ago. We need to be cautious about drawing general conclusions based on work with lab yeast strains.

The lab exercise based on the Ratcliff et al. (2012) paper [Experimental Evolution of Multicellularity] may be interesting but it's also misleading. The description of that experiment implies that students are reproducing the ancient evolution of multicellularity from single-cell organisms. Instead, what students are actually looking at is the reversion of a derived, exclusively single-cell strain, to the more primitive multicellular state. That's not the same thing.

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[Photo Credit: That's Ford at a rally in Ottawa where we were protesting the Conservative government's clamp-down on science in Canada. He took advantage of the audience to advertise his book.

Liu, H., Styles, C.A. and Fink, G.R. (1996) Saccharomyces cerevisiae S288C has a mutation in FL08, a gene required for filamentous growth. Genetics 144:967-978. [PDF]

Ratcliff, W.C., Denison, R.F., Borrello, M. and Travisanoa, M. (2012) Experimental evolution of multicellularity. Proc. Natl. Acad. Sci. (USA) 109:1595-1600. [doi: 10.1073/pnas.1115323109]