IDiots discover that RNA has secondary structure

I suppose we should be happy whenever some IDiots manage to educate themselves but somehow I find it quite sad when it takes thirty or forty years. Here's an example of a somewhat late-blossoming IDiot who posts on Evolution News & Views (sic): RNA Shows Design, Too. She doesn't sign her name to the post—I think I know why.

Here's what she just discovered ...

RNA differs from DNA in one of the sugars that makes up its backbone and one of the bases that makes up its side branches (uracil instead of thymine); it is also usually found in single strands instead of DNA's double helix. New discoveries, though, are showing RNA does far more than passively transfer DNA's information to other places. It, too, is a masterpiece of intelligent design and function.

A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression."

The paper by Rouskin et al. (2014) reports on the development of new software to detect secondary structure in RNA. This is news for IDiots who think that "new discoveries" show that RNA is capable of catalysis and other functions.

Think about that for a minute. This is 2014, it's 25 years since Sidney Altman and Tom Cech were awarded the 1989 Nobel Prize in Chemistry and more that 30 years since undergraduates were routinely taught about catalytic RNAs in introductory biochemistry courses. Those IDiots sure are slow learners.

In other words, the structure, not just the sequence, carries functional information.

Amazing. Sounds like they've never heard of the idea that ribosomal RNA catalyzes peptide bond formation and that it does so through secondary structure. They've never heard of self-splicing introns. All they have to do is read an introductory textbook of biochemistry or molecular biology.

Now if you connect this amazing new bit of information to the equally astonishing (not!) news that some lincRNAs have a function, you get this ....

More design found in what was formerly called junk; more information found parallel to existing information in RNA; more power found in the collective energy of intelligent agents. Why are you not surprised?

The real question is why are IDiots surprised by routine information that even high school students know?

And what does this have to do with intelligent agents? Has this person answered the quiz?

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Another day in New York

Our flight was canceled. We're spending another day in New York. Anyone want to meet for a beer or dinner?

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A quiz for those of you who think you understand Intelligent Design Creationism

One of the great ironies of the Intelligent Design Creationist movement is that its proponents don't understand evolution and they don't understand what their movement stands for. They can't agree on the meaning of intelligent design.

You might think I'm exaggerating about not understanding their own goals but just think about it for a moment. The movement encompasses people like Michael Denton who promote a deist version of creation and it also welcomes huge numbers of Young Earth Creationists who believe in the literal truth of the biblical creation myth. Many proponents are somewhere in between these extremes but the vast majority think that there's something seriously wrong with evolution that demands the intervention of an intelligent designer. The designer may have just made bacterial flagella and a few other complex molecular machines or he/she may have stepped in to make all the animal phyla. Almost every proponent of Intelligent Design Creationism thinks that the designer intervened in the human lineage to make humans special.

Someone named "nullasalus" thinks that it's only critics of Intelligent Design Creationism who are confused. He tries to set us straight at: A Quiz for Intelligent Design Critics.

In the near decade that I’ve been watching the Intelligent Design movement, one thing has consistently amazed me: the pathological inability of many ID critics to accurately represent what ID actually is, what claims and assumptions are made on the part of the most noteworthy ID proponents, and so on. Even ID critics who have been repeatedly informed about what ID is seem to have a knack for forgetting this in later exchanges. It’s frustrating – and this from a guy who’s not even a defender of ID as science.

I try really hard not to misrepresent the Intelligent Design Creationist movement. That includes my preference for adding the word "Creationist" to their label. What they're talking about is creationism—a being who creates the universe and who creates some aspects of living organisms.

It's never easy to say exactly what "the most noteworthy ID proponents" mean by intelligent design. That's because they can't agree among themselves. The most common characteristic is that they are all anti-evolution in one way of another. Some of them accept microevolution and some accept common descent but almost all of their writings focus on some aspect of evolution that they don't accept. It could be the idea of junk DNA, or the evolution of animals in the Cambrian, or any one of a long list of "icons of evolution" that scientists get wrong.

A great many prominent ID proponents are opposed to "materialism"—that means they support non-materialism, otherwise known as supernaturalism (e.g. founder Phillip Johnson). A great many prominent ID proponents try to paint all supporters of evolution as social Darwinists. They try to link us to Nazis and they go out of their way to denigrate Charles Darwin. This seems to be an integral part of the Intelligent Design Creationist movement and it can't be ignored.

Just read the titles of the major ID books. They are all about attacking evolution.

New friends in New York

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Pete Seeger (1919 - 2014)

Pete Seeger is dead. That means something to those of us who grew up in the 1960s. It was a time when opposition to war was so strong and so powerful that we thought it might bring an end to all wars.

We were so naive.

Peter Seeger wrote one of the most famous anti-war songs of all time, "Where have all the flowers gone." Peter, Paul, and Mary made it a big hit—and so did others. Here's Pete Seeger singing with them for the last time. This should be the anthem that marks the 100th anniversary of the beginning of World War I.

When will we ever learn?


We will be in Greenwich Village this weekend and I'll be thinking of Pete Seeger. Seeger also wrote "Turn! Turn! Turn!" Here's the best version by the Byrds: "A time for peace, I swear it's not too late."

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Hat Tip: Jerry Coyne

Seven things you need to know about evolution

John Hawks is a pretty cool guy. He studies anthropology with a special emphasis on the genetics of human evolution over the past million years or so. Right now he's in Ethiopia looking at fossils. I visited him a year ago at his lab in Madison, Wisconsin.

He written a summary of seven things about evolution. You should read what he has to say to see if you know enough about evolution. Here's a list of the seven things but each one requires a bit of explanation.

1. Evolution is change in a population
2. Evolution is genetic change
3. Many kinds of genetic changes are important to evolution
4. Evolution can be non-random
5. Evolution can be random, too
6. Populations evolve all the time
7. Evolutionary theory has changed a lot since Darwin's day

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Monday's Molecule #230

Last week's molecule was cholesterol [Monday's Molecule #229]. The figure shows how the molecule would look in a lipid bilayer (membrane). The winner was Tommy Stuleanu.

This week's molecule (below) is going to be hard. I won't be surprised if nobody gets the right answer. It's a key intermediate in an extremely important reaction. You need to give the common name AND the the overall reaction. Name the enzyme as well.

Email your answer to me at: Monday's Molecule #230. 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.)

Territorial demarcation and the meaning of science

Massimo Pigliucci doesn't get enough respect. He's upset by the "New Atheists" who place a great deal of emphasis on the scientific way of knowing and demand evidence that any other way of knowing is successful. These mean New Atheists (I count myself as one of them) use a very broad definition of science that includes most of the admirable activities of philosophers. Pigliucci is mostly a philosopher and he doesn't think that philosophy is getting enough respect from the New Atheists.

Here's the cartoon he published on his blog to illustrate the problem [see Rationally Speaking cartoon: Sam Harris].

Changing high school education: Equinox Summit and Learning 2030

I recently re-watched a program on The Agenda about high school education and what needs to be done to make it better. The broadcast was from the Perimeter Institute in Waterloo, Ontario, Canada and it featured the results of a conference on learning called the "Equinox Summit" organized by the Waterloo Global Science Initiative in collaboration with the Perimeter Institute. You can watch the final episode of the TV show at: The Agenda: What's Necessary? What's Possible?.

If you are interested in this subject, as I am, you should watch this show since it gives you a good perspective on what the "best minds" are thinking. You can make up your own mind about whether this is encouraging or not.

Here's a short video on the summit ...



The communique from Equinox Summit: Learning 2030 isn't very long so you can read it quickly. Here are the goals that this group decided on.

In order for high school graduates to reach their full potential in life, they need to be:

• lifelong learners who can identify and synthesize the right knowledge to address a wide range of challenges in a complex, uncertain world
• literate, numerate, and articulate
• creative, critical thinkers
• able to collaborate effectively with others, especially those of different abilities and backgrounds
• open to failure as an essential part of progress
• adaptable and resilient in the face of adversity
• aware of the society they live in and able to understand the different perspectives of others
• self-aware and cognizant of their own strengths and limitations
• entrepreneurial, self-motivated, and eager to tackle the challenges and opportunities of their world

To achieve these goals, we require a radically di fferent structure for learning in 2030, one in which traditional concepts of classes, courses, timetables, and grades are replaced by more flexible, creative and student-directed forms of learning. This develops deep conceptual understanding, which can then be applied in other contexts.

There's nothing radical about these goals. They're pretty much the same goals that any conference in the 1960s would have come up with. The only really new buzzword is "entrepreneurial"—that's borrowed from business and it wouldn't have been popular in the 1960s. Today every high school student has to be an entrepreneur because by 2030 nobody will be working for anyone else. They'll all be running their own businesses.¹

I've been trying to teach creative and critical thinking for a long time and I haven't come up with any really good ideas. It's probably because I'm too old. You should watch the Agenda show to see how young people are going to solve these problems.

But here's a question that occurs to me as I'm thinking critically about this problem. Let's assume that we can achieve all those goals. Let's assume that in order to graduate from high school you have to have learned how to think critically; be literate, numerate, and articulate; be able to collaborate, be entrepreneurial, be adaptable, etc.

They are laudable goals that I support, but what percentage of students entering high school can achieve them? I'm thinking that, with lots of resources and excellent teachers, it might be possible for about 50% of high school students to reach these lofty goals. The rest are going to achieve the goals of learning to be "open to failure as an essential part of progress" and how to be "adaptable and resilient in the face of adversity."

I think we might have trouble convincing most societies, and most governments, that a 50% graduation rate from high school is the price of higher standards.

I'm not even sure that all of the students graduating from the University of Toronto are literate, numerate, articulate, critical thinkers.

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1. This will save enormous amounts of tax dollars because nobody will be working for the government.

Has John Brockman's stable lost its edge?

John Brockman is a famous literary agent. Over the years he has assembled a group of intellectuals, and people who aspire to be intellectuals. Every year they publish short articles on the question of the year at the Edge. Here's this year's question: annual question.

Science advances by discovering new things and developing new ideas. Few truly new ideas are developed without abandoning old ones first. As theoretical physicist Max Planck (1858-1947) noted, "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it." In other words, science advances by a series of funerals. Why wait that long?

WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT?
Ideas change, and the times we live in change. Perhaps the biggest change today is the rate of change. What established scientific idea is ready to be moved aside so that science can advance?

There was a time—about a decade ago—when reading the answers to the question was exciting and stimulating.

Jerry Coyne picks two answers that deal with evolution: The Edge question: two bad answers about evolution. Roger Highfield's answer to the question of what idea should be retired is "Evolution is true." Kevin Kelly thinks that the idea of "Fully random mutations" should be tossed in the scrap heap of history.

Jerry shows us why these guys are not intellectuals. Read his blog post.

Lest you think that Jerry found the only bad examples, let me point out another one. Athena Vouloumanos is a psychologist at New York University. The idea that she wants to retire is "Natural Selection is the Only Engine of Evolution." Excellent, I thought, at last somebody has a good answer. Alas, here's what she says ...

Epigenetic control of gene expression contributes to cells in a single organism (which share the same DNA sequence) developing differently into e.g. heart cells or neurons. But the last decade has shown actual evidence–and possible mechanisms–for how the environment and the organism's behavior in it might cause heritable changes in gene expression (with no change in the DNA sequence) that are passed onto offspring. In recent years, we have seen evidence of epigenetic inheritance across a wide range of morphological, metabolic, and even behavioral traits.

The intergenerational transmission of acquired traits is making a comeback as a potential mechanism of evolution. It also opens up the interesting possibility that better diet, exercise, and education which we thought couldn't affect the next generation–except with luck through good example–actually could.

If I had to give a reason why natural selection is not the only engine of evolution I would have picked something very different—something that's been around, and proven, for decades. Epigenetics requires DNA sequences and proteins and if epigenetic modification of a specific DNA site provides a selective advantage under some circumstances then that's natural selection in action.

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Chesterton Debate Series: Is There a God?

The Centre for Inquiry Canada is promoting an upcoming debate between Justin Trottier and Philip Cleevely on the topic "Is There a God."

We know the answer but it still promises to be a fun evening. All the cool people will be there. I'm going to be there too. Email me if you want to join us for dinner before the event. I'll invite some of the cool people like Veronica Abbass and Kevin Smith.

CLICK HERE TO REGISTER

At the first event of the series, Fr. Philip Cleevely (Catholic priest and philosophy professor) and Justin Trottier (founder of the Centre for Inquiry Canada) will argue the question, "Is There a God?" The debate will be moderated by Stephen LeDrew (host/commentator of CP24).

Date: Friday, February 7 from 7:00-9:30pm

Venue: Isabel Bader Theatre (Victoria University)
              93 Charles Street West, Toronto

Registration: Limited seating. Tickets cost $10. Click here to register.

Biographies:

Fr. Philip Cleevely, C.O. was born in England in 1966. Educated in English Literature and Philosophy at Oxford and Cambridge Universities (UK) and in Toronto, he joined the Catholic Church in 1989. For years later, he entered a religious community in Birmingham, England called the Oratory of St. Philip Neri. Following theological studies in Rome, he was ordained to the priesthood in 2001. At the beginning of 2011, he transferred permanently to the Oratory community in Toronto, where he teaches Philosophy and Theology at St Philip’s Seminary.

Justin Trottier is Founder and Ambassador for the Centre for Inquiry Canada, an educational charitable organization advancing science and secularism. He is a board member of the Canadian Secular Alliance and a regular spokesperson on church-state separation, skeptical inquiry and fundamental freedoms. He hosts Think Again! TV, appears regularly on the John Oakley Show’s Culture War on AM640 Toronto radio and the Conspiracy Show on Vision TV, and publishes on the National Post’s religion blog. He ran as a candidate in the 2011 Ontario provincial election. With a passion for science education, Justin also hosts The Star Spot, a space sciences themed podcast and radio show

After-party:
After the event, all of our atheist, freethinking, and skeptical members, guests and friends are invited to join us at:

Gabby’s Bar & Grill
192 Bloor Street West
Toronto
ON M5S 1T8

Keep the discussion going on our Facebook Page.

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The Biology of Faith and Religion

Rufina Kim has re-started the discussion group we had last year. Join us for an evening of interesting conversation in room 5243 on the 5th floor of the Medical Sciences Building at the University of Toronto (Toronto, Canada). Bring your own food and beverage. The date is Wednesday, January 29, 2014 and the time is 6pm.

Everyone is welcome. You don't have to be a student or a faculty member to attend. Add your name to the list on Facebook at The Biology of Faith and Religion.

Is there a God? Why is the majority of the global population religious (and why are some not)? Why does religious faith lead to resistance in the face of scientific evidence? Why are research findings in evolutionary biology and cosmology still contentious among the public, while those in chemistry and physiology are not? What are the implications of religious belief in scientific progress?

These are some of the questions we will delve into at our next Thoughts on Science (TOS) meeting. Individuals of all worldviews are encouraged to attend to enlighten and be enlightened.

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Extreme cold weather

I live in Canada. It's winter. It gets cold. During the night it's about -20°C¹.

It seems like everyone in the city of Toronto is yacking about the "extreme" cold weather we're having.

People in Saskatoon and Edmonton are laughing at us. So are people in Ottawa and Montreal. It's embarrassing.

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1. That's -4°F if you live in Belize or the United States of America.

William Reville attacks scientism

John Wilkins linked to essay by someone named William Reville on "Philosophers must oppose arrogance of scientism." Reville is not a philosopher—he's a retired biochemist and Public Awareness of Science Officer from the University College Cork in Ireland.

He writes a regular column for The Irish Times on the relationship between science and religion. He's a Roman Catholic.

I'm interested in the conflict between science and religion and I usually pay attention to anything that John Wilkins recommends so I looked at this article. I think it might be fun to examine it to see how some theists think about the issue. Let's see how he starts out ...

The problem of anonymity on the internet

There's a little kerfluffle in the blogosphere because an anonymous blogger has been outed. Michael Eisen posted an interesting comment of the episode and I want to add my 2 cents to something he says at: On anonymity in science and on Twitter. Here's the part I want to address ...

A lot of people who I interact with on Twitter, and whose blogs I read, have chosen to tweet and write under pseudonyms. This puzzled me at first, but I have come to realize that there are a LOT of good reasons for people to mask their real identities online.

Anonymity allows people to express their opinions and relate their experiences without everything they say becoming part of their personal permanent record. It affords people who are marginalized or in tenuous positions a way to exist online without fear of retribution. Pseudonyms help create a world where ideas matter more than credentials. And they provide some kind of buffer between people – especially women – and the nastier sides of the internet.

The myriad and diverse pseudonymous voices out there make the internet a richer and more interesting place. Maybe it’s weird, but I consider many of these people whom I’ve never met and whose real identities I don’t know to be my friends.

Here's the problem. I agree with everything that Michael says but there's still something about hiding behind a pseudonym that makes me uneasy. I much prefer dealing with people who use their real names. I grew up believing that it was admirable to stand up and be accountable for your beliefs and opinions no matter what the consequences.

Yes, I'm well aware of the fact that it's a lot easier for a tenured professor to say this than for someone who is in a much more vulnerable position. Michael Eisen also knows this—read his post. That's part of the problem. We understand that the "consequences" of speaking out against authority can be quite severe and we both understand that there's value in hearing from certain anonymous voices.

I guess where I differ from Michael Eisen is that right now I don't think I follow any blogger whose identity isn't known to me. It may be true in theory that ideas matter more than identity but, in reality, there just aren't very many examples. On the other hand, there are lots of examples where people use anonymity to say things they would never say in public even if their identity was concealed.

Does the upside of anonymity make up for the downside? That's the real question. I don't know the answer but I'm leaning toward "no."

I'd like to live in a society where you could never be punished for anything you say or believe. It makes me uneasy to live in a society that accepts the idea that you will be punished for your opinion and sets up ways of permitting people to say whatever they want without having to face any consequences. It seems like that's a way of giving up on the fight for freedom of expression and legitimizing the idea of systemic intolerance.

I try to get my students to speak up during class and express their views and opinions. I think it's an essential component of learning how to think critically. I try and get them to write essays where they defend a controversial idea, even if it's unpopular. I don't think it's a good idea if it becomes the accepted norm that you can only do this if you can be assured that nobody will find out who you are.

(I know most of the people who comment on Sandwalk but there are some who use pseudonyms. There's a good correlation between people who comment anonymously and those whose ideas don't deserve respect. There's also a powerful correlation between those who use their real names and those ideas are worth listening to even if they disagree with mine.

That's doesn't mean you shouldn't comment using a pseudonym. Just be aware of the company you're keeping.)

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