Learning About Evo-Devo

We talked about evolutionary developmental biology (evo-devo) in my class last week. The main issue is whether the proponents of evo-devo are making a substantive contribution to evolutionary theory. Is evo-devo going to be part of an extended modern synthesis, and, if so, how? My own view, which I express to the class, is that the discoveries of developmental biology pretty much confirm what Stephen J. Gould wrote in Ontogeny and Phylogeny back in 1977.

What, then, is at the root of our profound separation? King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation: small changes in the timing of development can have manifold effects upon a final product "Small differences in the timing of activation or in the level of activity of a single gene could in principle influence considerably the systems controlling embryonic development. The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts." Differences in regulation may evolve by point mutations of regulatory genes or by rearrangement of gene order caused by such familiar chromosomal events such as inversion, translocation, fusion, and fission. Studies of banding indicate that at least one fusion and ten large inversions and translocations separate chimps and humans.

Stephen J. Gould (1977) Ontogeny and Phylogeny, Harvard University Press, Cambridge Massachusetts, USA pp. 405-406

This helps us understand the history of life, especially the evolution of animals, but it doesn't contribute to evolutionary theory.

PZ Myers is teaching a developmental biology course and his students are dealing with three take-home questions this weekend [What I taught today: O Cruel Taskmaster!]. I'd like to reproduce two of them here since they're very relevant to the debate over the importance of evo-devo.

Question 1: One of the claims of evo devo is that mutations in the regulatory regions of genes are more important in the evolution of form in multicellular organisms than mutations in the coding regions of genes. We’ve discussed examples of both kinds of mutations, but that’s a quantitative claim that won’t be settled by dueling anecdotes. Pretend you’ve been given a huge budget by NSF to test the idea, and design an evodevo research program that would resolve the issue for some specific set of species.

I'd like my students to keep in mind Richard Lenski's ongoing evolution experiment in E. coli. Recall that evolution of the ability to grow on citrate depended mostly on mutations that changed the regulation of citrate utilization genes.

Since we have many examples of mutations that affect regulation of gene expression in bacteria, yeast, and other single-cell organisms, why do the proponents of evo-devo think they're on to something special when they look at development in animals? What is there about the evolution of "form" that changes our views on evolution?

Question 2: Every generation seems to describe the role of genes with a metaphor comparing it to some other technology: it’s a factory for making proteins, or it’s a blueprint, or it’s a recipe. Carroll’s book, Endless Forms Most Beautiful, describes the toolbox genes in terms of “genetic circuitry”, “boolean logic”, “switches and logic gates” — he’s clearly using modern computer technology as his metaphor of choice. Summarize how the genome works using this metaphor, as he does. However, also be aware that it is a metaphor, and no metaphor is perfect: tell me how it might mislead us, too.

Before answering PZ's question about Sean Carroll and metaphors, I'd like my students to remember the quotation I gave them in class. Discuss the use of hyperbole and metaphor in this context.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

This book tells the story of this new revolution and its insights into how the animal kingdom has evolved. My goal is to reveal a vivid picture of the process of making animals and how various kinds of changes in that process have molded the different kinds of animals we know today and those from the fossil record.

Sean B. Carroll Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton & Co., New York (2005) p. x

I'd also like Sandwalk readers to keep in mind the recent ENCODE publications. They talked extensively about genetic circuits and regulation. In fact, their major "finding" was the idea that our genome is full of regulatory elements; so many, in fact, that most of what we thought was junk DNA is actually part of a a vast control circuit. Has this emphasis on a multitude of switches and controls been misleading or is it turning out to be correct?

I would ask a third question. The evolution of toolkit genes (i.e. transcription factors) make it possible to evolve many different body plans with only a small number of mutations. It helps explain the Cambrian explosion. Given our current understanding of evolution, is it possible to select for a evolution of a toolkit that has this potential for future evolution? Explain your answer.

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ENCODE, Junk DNA, and Intelligent Design Creationism

andyjones has replied to my earlier posting on ENCODE and junk DNA. You can read his response at: (More) Function, the evolution-free gospel of ENCODE. Here's part of what he says ...

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither.

It's true that there are some IDiots who are distancing themselves from a commitment to junk DNA. There are probably some who claim that they could live with the fact that 90% of our DNA is junk.

But let's not forget that Jonathan Wells is a prominent IDiot and he wrote a book on The Myth of Junk DNA. It sounded very much like Intelligent Design Creationism is staking its reputation on finding function for most of our genome.

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The Hardy-Weinberg Equilibrium

It's important to understand modern evolutionary theory and that means it's important to understand the Hardy-Weinberg Equation and what it means.

The significance is explained in all the leading textbooks on genetics and evolution. I've chosen the explanation given by Carl Zimmer and Douglas Emlen because I know that Carl has spent a good deal of time getting it right in his new book Evolution: Making Sense of Life.

Imagine that you have a population with two alleles, A and a, at a single locus. The frequency of the first allele is f(A) to which we assign the value p. The frequency of the second allele is f(a)=q. In a randomly mating sexual population the probability of an A sperm being produced is p and the probability of an a sperm being produced is q. Similarly, the probability of an A egg cell is p and the probability of an a egg cell is q. These probabilities, p and q, do not have to be equal.

We can calculate the probabilities of all possible combinations or sperm and eggs in the population from a the following diagram (Punnett square). This one is from Wikipedia.


Since the total probability has to equal one, we have ....

p² + 2pq + q² = 1

This is the Hardy-Weinberg equation or the Hardy-Weinberg Equilbrium. What does it mean? Let's quote Zimmer and Emlen (page 156).

Hardy and Weinberg demonstrated that in the absence of outside forces (which we describe later), the allele frequencies of the population will not change from one generation to the next. As we'll see below, this theorem is a powerful tool for population geneticists looking for evidence of evolution in populations. But it's important to bear in mind that it rests upon some assumptions.

One assumption of the model is that a population is infinitely large. If a population is finite, allele frequencies can drift randomly from generation to generation simply due to chance variation, in which alleles happen to be passed on to the next generation. (We will explore genetic draft in detail later in the chapter.) While no real population is infinite, of course, very large ones behave quite similarly to the model. That's because variation due to chance is inconsequential, and the allele frequencies will not change very much from generation to generation.

The Hardy-Weinberg theorem also requires all of the genotypes of the locusts are equally likely to survive and reproduce. If individuals with certain genotypes produced twice as many offspring as individuals with other genotypes, for example, then the alleles that these certain individuals carry will comprise a greater proportion of the total in the offspring generation than would be expected given the Hardy-Weinberg theorem. In other words, selection for or against particular genotypes may cause the relative frequencies of alleles to change and results in evolution.

Yet another assumption of the Hardy-Weinberg theorem is that no alleles enter or leave a population through migration. This assumption can be violated in a population if some individuals disperse out of it or if new individuals arrive. The model also assumes that there is no mutation in the population, because it would lead to new alleles

In each of these four cases, the offspring genotype frequencies will differ from the equilibrium predictions of the Hardy-Weinberg theorem. That is, because they alter allele frequencies from one generation to the next, selection, migration, and mutation are all possible mechanisms of evolution.

The Hardy-Weinberg theorem is useful because it provides mathematical proof that evolution will not occur in the absence of selection, drift, migration, or mutation. By explicitly delineating the conditions under which allele frequencies do not change, the theorem serves as a useful null model for studying ways of allele frequencies do change. The Hardy-Weinberg theorem helps us understand explicitly how and why populations evolve. By studying how populations deviate from the Hardy-Weinberg equilibrium, we can learn about the mechanisms of evolution.

There you have it. The Hardy-Weinberg describes the situation where evolution DOES NOT HAPPEN and thus serves as the null hypothesis for testing whether evolution is happening. Every undergraduate knows this.

Let's see if the Intelligent Design Creationists know this. I'm quoting "niwrad" from a post on one of the leading ID websites, Uncommon Descent: The equations of evolution.

For the Darwinists “evolution” by natural selection is what created all the species. Since they are used to say that evolution is well scientifically established as gravity, and given that Newton’s mechanics and Einstein’s relativity theory, which deal with gravitation, are plenty of mathematical equations whose calculations pretty well match with the data, one could wonder how many equations there are in evolutionary theory, and how well they compute the biological data related to the Darwinian creation.

....

The Hardy-Weinberg law mathematically describes how a population is in equilibrium both for the frequency of alleles and for the frequency of genotypes. Indeed because this law is a fundamental principle of genetic equilibrium, it doesn’t support Darwinism, which means exactly the contrary, the breaking of equilibrium toward the increase of organization and creation of entirely new organisms. To claim that the Hardy-Weinberg law explains evolution is as to say that in mechanics a principle of statics (immobility) explains dynamics (movement and the forces causing it).

....

So the initial question, how well math support Darwinian evolution, has the short answer: it doesn’t support evolution at all. Despite of the pretension of evolution to be a scientific theory with the mathematical certitude of the hard sciences, properly the equations of evolution do not exist.

As you can see, the Intelligent Design Creationists interpret the "Hardy-Weinberg law" very differently, I wonder who is right?

Let's check with Joe Felsenstein. He's an expert on population genetics so he should know. Read his decision at: Evolution disproven — by Hardy and Weinberg?.

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He Likes Me ... He Really Likes Me!

David Klinghoffer likes me and he's not afraid to say so [Laurence A. Moran, University of Toronto Biochemist and Darwin Skeptic]. He says,

Welcome aboard, Dr. Moran! The U. of Toronto biochemist surprised us by indicating in a post at his Sandwalk blog that he could sign on to the statement in the Scientific Dissent from Darwinism ....

Let me remind readers what the statement says ...

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

Just about every evolutionary biologist would have to agree with this statement if they were being honest. So why is this such a big deal for the Intelligent Design Creationists? Why do they promote their list of signatories in their publications and why do they continue to solicit signatures on their website? [A Scientific Dissent from Darwinism]

David Klinghoffer has the answer. Do you believe him?

... no one says that the signers of the Dissent list are creationists, other than Darwin advocates who dishonestly try to cement the absurd, fallacious equation of Darwin skepticism with Young Earth Creationism. The list has nothing to do with creationism. Nor does it say anything about intelligent design, which also has nothing to do with creationism.

Okay, so the list has nothing to say about intelligent design. So what is its real purpose?

Any scientist who agrees with the statement that heads the Scientific Dissent from Darwinism is a Darwin doubter, that's all -- and congratulations to him or her! Simply to relay the fact of his skepticism on orthodox evolutionary theory is hardly a misuse of anyone's name. It just reports some interesting and good news. What's wrong with that? For Darwin defenders, the thing that's wrong is that it undercuts their main defense: the assertion that nobody doubts Darwin's theory, or only religious nuts do so, and so there is no legitimate controversy on evolution.

We've always said that private doubts about Darwinian theory are far more widespread in scientific life than the media let on. Now on that point we have Dr. Moran's helpful confirmation.

Hmmm ... that's what this is all about? The IDiots know full well that most evolutionary biologists aren't strict Darwinists but they just want this to become more widely known? If that's true then they could certainly help out by explaining the correct version of modern evolutionary theory—including random genetic drift— to their supporters and advising them not to use the term "Darwinism" as a synonym for "evolution." That would make sense, right?

From now on, I expect David Klinghoffer and all his friends to use "modern evolutionary theory" to describe the position of their opponents. I expect them to avoid the word "Darwinism" since, by their own admission, they know that it's wrong.

Not holding my breath .....

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The title of this post is a reference to a statement by Sally Field

at her Oscar acceptance speech in 1985. I know that I'm paraphrasing a misquote.

Doug Axe Challenges Darwinian Evolution

Here's a video where Douglas Axe tries to explain why Darwinism is wrong. I'm going to let Sandwalk readers discuss the many flaws in his argument but first I want to mention two things.

1. Jeffrey Shallit shows that his statements about information theory are about as accurate as his statements about evolution. [Doug Axe Doesn't Understand Information Theory]
2. Like most IDiots, Doug Axe continues to equate Darwinism and natural selection with evolution. He does this in spite of the fact that his colleague, Ann Gauger, claims to understand the difference. According to her, scientists who doubt Darwinism can still be firm supporters of evolution. If the IDiots actually believe this then why do they keep using the term "Darwinism" to describe their opponents?

The bit about junk DNA in the video reveals that Doug Axe doesn't known dick about evolution or Darwinism. The version of evolution known as Darwinism rejects the idea that most of our genome is junk. I don't think Doug Axe can handle that kind of truth.



Remember folks, this is just about the best they have to offer.

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Call for Papers: Observing the Scribe at Work

Observing the Scribe at Work: Knowledge Transfer and Scribal Professionalism  in Pre-Typographic Societies

Macquarie University, Sydney

27-28 September 2013

Prior to the typographic revolution of the 15th century, the figure of the scribe was one of the keys by which civilisations were able to disseminate their power, culture and beliefs beyond their geographic, temporal, and even linguistic limits. Our access to the pre-modern world is mediated by the material and technological remains of scribal activity, the manuscript as an artefact of culture and administration. Every text preserved prior to the advent of printing bears witness to the activities of scribes. Yet as a social and professional group they are frequently elusive, obscured by other professional titles, reduced to mention in a colophon, or existing within a private sphere into which our sources do not reach. While much attention has been given to the scribe as a literary figure, the manuscripts offer a unique point of access to this group without the distortions of the literary tradition. This perspective, however, has frequently been restricted to a catalogue of errors, reducing the scribe to the transmission of an acceptable text, without recourse to the physical characteristics of the manuscript itself.

This workshop is built around the Australian Research Council funded project ‘Knowledge Transfer and Administrative Professionalism in a Pre-Typographic Society: Observing the Scribe at work in Roman and Early Islamic Egypt’. The project sets aside the often futile search for the historical figures of the scribe in favour of a focus on observable phenomena: the evidence of their activity in the texts themselves. Recognizing that the act of writing can be a quotidian and vernacular practice, it explicitly includes the documents of everyday life as well as the realms of the copying of literature, seeking paths back to an improved understanding of the role and place of scribes in pre-modern societies.

‘Observing the Scribe at Work’ will bring together specialists in pre-modern societies of the Mediterranean world and adjoining cultures, from the ancient Near East, through the Egyptian and Classical worlds to Byzantium and Renaissance Europe. The papers will contribute to a deeper understanding of the processes that drive the operation of pre-printing cultures, and transmit knowledge and traditions forward in human societies.

The workshop will be held at Macquarie University on 27-28 September 2013. Macquarie University cannot offer full funding for all participants traveling to Australia from overseas, but partial financial assistance will be awarded to select abstracts which closely address the themes of the workshop. Decisions to this effect will be made by the end of April.

We call for abstracts of up to 300 words that address the objectives of this workshop. These should be sent to jennifer.cromwell@mq.edu.au by 31 March 2013.

 Inquiries: Malcolm Choat (malcolm.choat@mq.edu.au); Jennifer Cromwell (jennifer.cromwell@mq.edu.au)

Organising Committee

Malcolm Choat, Jennifer Cromwell, Korshi Dosoo, Rachel Yuen-Collingridge

Sponsors

Australian Research Council

Macquarie University

Faculty of Arts, Macquarie University

Macquarie University Ancient Cultures Research Centre

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I'm a New Friend of Ann Gauger

A few days ago I posted a message about the IDiots' list, A Scientific Dissent from Darwinism, of people who disagree with Darwinism. I specifically mentioned Joshua Youngkin who said that, " 'A Scientific Dissent from Darwin,' is a thorn in the side of those who say there's no scientific debate over whether evolution works in a completely naturalistic fashion." [Our "Scientific Dissent from Darwin" List: A Reader Inquires] Let's be clear about what he said, he said that the list reveals scientific debate over whether "evolution works in a completely naturalistic fashion." In other words, people who sign the list must be non-naturalists. That's another word for creationist.

Here's the statement ...

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

Note that the statement says noting about whether evolution works in a completely naturalistic fashion. The IDiots know full well that most scientists would agree with the statement taken at face value but we all know that the IDiots will misuse the statement just as Joshua Youngkin did on the Evolution News & Views blog. You can find further proof of the treachery of the IDiots at the list website where the following quote from someone named Raul Leguizamon is prominently featured on the home page.

I signed the Scientific Dissent From Darwinism statement, because I am absolutely convinced of the lack of true scientific evidence in favour of Darwinian dogma. Nobody in the biological sciences, medicine included, needs Darwinism at all. Darwinism is certainly needed, however, in order to pose as a philosopher, since it is primarily a worldview. And an awful one, as George Bernard Shaw used to say.

The implication is clear.

Ann Gauger is thrilled to discover that I'm not a Darwinist [Our New Friend, Laurence A. Moran]. I guess she's under the impression that if you're not a Darwinist then you must be an IDiot like her.

Here's how her mind works ...

1. People on the Dissent from Darwinism list are supporters of the statement.
2. Larry also agrees with the dissent statement.
3. Larry says only IDiots claim that supporters of this statement are creationists.
4. Larry says that Project Steve is a excellent parody of the "creationist" list, thus in effect calling supporters of the statement creationists.

Wait. Following the logic there, that would seem to make Dr. Moran an IDiot, in his own eyes anyway. Not that, in pointing this out, I mean it unkindly.

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Who Owns Your Genome?

The sequence of your genome contains lots of information about you. It also contains lots of information about your parents, your siblings, and your children. That's why you should not make your genome sequence public without obtaining their permission.

The sequence of Henrietta Lacks' genome was just published (HeLa cells) and nobody bothered to seek permission from her survivors. Jonathan Eisen has a comment and he has also collected all the information on the internet [HeLa genome sequenced w/o obtaining permission/consent from family - some comments and background]. Be sure to read the New York Times article by Rebecca Skloot: The Immortal Life of Henrietta Lacks, the Sequel. She says,

LAST week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours.

In my opinion, there is no excuse for publishing this genome sequence without consent.

Razib Khan disagrees. He thinks that he can publish his genome sequence without obtaining consent from anyone else and I assume he feels the same way about the sequence of the HeLa genome [Henrietta Lacks’ genome, and familial consent].

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Do Invertebrates Really Make Up 80% of All Species on Earth?

bug_girl has a new post called Planet of the Arthropods. She asks why we should care about invertebrates, "Why should we care about a bunch of squishy boneless animals? Because invertebrates make up EIGHTY PERCENT OF ALL THE SPECIES ON EARTH. They truly are the 'little things that run the world.'"

She links to this image ...


Isn't that amazing! Single-celled eukaryotes, fungi, and bacteria make up such a small percentage of total species (<1%) that they don't even register on this summary!

Here's a phylogeny of eukaryotes (no bacteria) from Keeling et al. (2005). If you look closely, you can find "animals" down in the lower right-hand corner. Isn't it amazing that one little insignificant branch represents 83% of all species on the planet? Seriously, something is wrong with taxonomy if this is even close to being true.


Estimates of the total number of bacterial species range from about one million to about one billion [Jonathan Eisen]. Read Carl Zimmer's New York Times article: How Many Species? A Study Says 8.7 Million, but It’s Tricky for an interesting perspective.

The general public has a very poor understanding of our relationship to all other species on this planet. We should be working hard to dispel the major misconceptions about biology and evolution.

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Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676. [doi:10.1016/j.tree.2005.09.005]

Estimating the Human Mutation Rate: Direct Method

This is the fourth in a series of posts on human mutation rates and their implication(s). The first three were ...

What Is a Mutation?
Estimating the Human Mutation Rate: Biochemical Method
Estimating the Human Mutation Rate: Phylogenetic Method

There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method.

The Biochemical Method is based on our knowledge of biochemistry and DNA replication as well as estimates of the number of cell divisions between zygote and egg. It gives a value of 130 mutations per generation. The Phylogenetic Method depends on the fact that most mutations are neutral and that the rate of fixation of alleles is equal to the mutation rate. It also relies on a correct phylogeny. The Phylogenetic Method gives values between 112-160 mutations per generation. These two methods are pretty much in agreement.

The Direct Method involves sequencing the entire genomes of related individuals (e.g. mother, father, child) and simply counting the new mutations in the offspring. You might think that the Direct Method gives a definitive result that doesn't rely on any assumptions, therefore it should yield the most accurate result. The other two methods should be irrelevant.

This would be true if the Direct Method were as easy as it sounds but things are more complicated.

Read more »

Michele Bachmann Lies About Socialized Medicine

Michele Bachmann is an IDiot but I try to avoid commenting on the fact that she's a duly-elected congresswoman from Minnesota. If Americans want to elect someone like her to run their country then that's up to them.

People in the civilized world outside of the USA are puzzled by some of the things she says—they wonder how she can get away with such statements and still be elected. Her recent speech on "Obamacare" in Congress is a case in point. You can see it in the video below. This is the speech where she says, ""Repeal this failure [Obamacare] before it literally kills women, kills children, kills senior citizens."


Later on her spokesman, Dan Kotman, issued the following statement.

Obamacare is forcing doctors into the employ of cost-cutting hospitals, gives government the authority to determine services that will and will not be covered, has a board independent of Congress that can cut payments for care, and allows the Secretary of Health and Human Services to force all health plans to eliminate any doctor that doesn't practice medicine the government's way. The history of government-run health care systems around the world is a history of denial, delay and sadly even death.

It's one thing to attack "Obamacare" but when she attacks healthcare in Canada and all other civilized countries, that's a different issue.

Let me remind you that there's tons of data showing that people live longer in other countries and they survive cancer better. Infant mortality is lower in other countries. And this success is achieved at lower cost than health care in the USA. In other words, Michele Bachmann is dead wrong when she says that socialized medicine is a "history of death."

As I was preparing this post I stumbled across a video of Senator Jeff Sessions of Alabama defending American health care in the Senate of the United States Congress. Are Americans embarrassed by speeches like this or is this typical of Americans who have been elected to the Senate? Is it the best that Alabama has to offer?

Sen. Jeff Sessions: 'So We've Got People Who Die Sooner'

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Mocking Friedman's MOOCs

Thomas L. Friedman is the Op-ed columnist for foreign affairs at the New York Times. He has won three Pulitzer Prizes (1983, 1988, 2002).

According to Wikipedia, Friedman has an undergraduate degree from Brandeis University (Boston, USA) and a Master's degree from Oxford (UK). He taught a class at Brandeis in 2006 but as far as I can tell that's his only experience with university outside of being a student. He does not appear to be an educator and he doesn't appear to have any expertise in pedagogy.

That hasn't prevented him from writing three opinion pieces on the imminent demise of universities and the glorious future of online courses—especially MOOCs (Massive Open Online Courses).

Come the Revolution May 15, 20012
Revolution Hits the Universities January 26, 2003
The Professors’ Big Stage: March 5, 2013

Read more »

Goodbye John Witton

I'm rather proud of the fact that few people have been banned from this blog. That's why it's worth a special post when someone gets banned.

John Witton can no longer post comments on Sandwalk. He has proven that he is a liar when he backed out of his offer to pay $1000 to anyone who would answer his questions [John Witton Will Pay You $1000 to Answer One of His Questions].

More importantly, he continues to spam the comments sections of several posts. Nothing that he says is relevant to the topic and many of his recent comments are delusional.

Goodbye John Witton.

He joins a special group of people who have been banned from Sandwalk: Joe (Joseph) Bozorgmehr (Atheistoclast), David Roemer, and Douglas Dobney. The fastest and easiest way to get banned is to try and intimidate me (or any other blogger) by writing nasty letters to our employers and/or bosses. That's how David Roemer, and Douglas Dobney got banned. Equally efficient is to post lots of comments attacking my integrity and accusing me of all sorts of vile (untrue) things (Atheistoclast). Witton took the slow route to being banned.

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Estimating the Human Mutation Rate: Phylogenetic Method

This is the third in a series of posts on human mutation rates and their implication(s). The first two were ...

What Is a Mutation?
Estimating the Human Mutation Rate: Biochemical Method

There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method¹.

The phylogenetic method relies on a known phylogenetic tree to pick out close relatives and the approximate time to the last common ancestor. In the case of humans, we know that chimpanzees and bonobos are our closest cousins and we think that the homind line diverged from the chimp line about 5 million years ago.

Read more »

On the Effectiveness of Ridicule and Mockery

From time to time we hear from religious people who are upset about the way we treat their faith. They claim that by making fun of their logic and their defense of god we are only making religious people more convinced that they are right. According to them, we'll never convince any religious person to abandon god(s) by using ridicule and mockery.

Perhaps that's right but I very much doubt it. Here's Sam Harris illustrating the power of ridicule to make a point.

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[Hat Tip: lutesuite]

ENCODE & Junk and Why We Call Them IDiots

The Intelligent Design Creationists have been following the debate over the ENCODE results. For them this is a serious issue since they are committed to the idea that well-designed genomes should not be full of junk. You'd think that the IDiots would make an attempt to learn the real scientific issues at stake.

Let's see how andyjones does on Uncommon Descent: Function, the evolution-free gospel of ENCODE. He says,

Apparently, ENCODE are to be criticised for using an ‘evolution-free’ definition of function. Yep, you heard that right. You thought that function was function was function, but oh no, you must use a evolution-y definition or you will not get the ‘correct’ evolution-y answer. It seems awfully like you need to presuppose Darwinism or you will not find Darwinism. Can that be right?

The excuse for this is some interesting Darwinian philosophy (or do I mean sophistry? – make up your mind below): the authors believe that function means nothing (is purely subjective) unless it is selected for. For example, the heart causes the pericardium (the membrane around the heart) to not collapse by filling space, so we could call that a function, but it is selected for pumping blood.

....

Amongst other things the ENCODE authors are lambasted for not distinguishing between ‘Junk DNA’ and ‘Garbage DNA’. No seriously, ‘junk’ now means stuff that is functional, but not used very often, but could be used, like stuff in your attic is ‘junk’. It is different from ‘garbage’, which is the stuff that you would put straight in the bin. ‘junk’ is now a rather misleading word for ‘functional’. So our genome is full of ‘junk’ that is useful and functional, but to a Darwinian it does not count until it starts getting used so that natural selection can get the credit. How convenient! The possibility of design is sidestepped by careful choice of language. Welcome to 1984! A better word might be ‘archived’ rather than ‘junk’.

...

I, and many of us, hold to an ID worldview firstly and most securely because of what we know about prebiotic chemistry and thus the origin of the first life form. Based on that, because I know there has been a designer involved, I think probably a lot of ‘junk’ will turn out to be ‘brought down from the attic’ at various stages of an organisms life, especially in the developing stages. Time will tell.

Scientific means finding out what is actually there. ENCODE are to be praised for doing that. Darwinism has always been about telling creation myths from the point of view of naturalism (roughly, physics only), and shoehorning every fact into the story. ENCODE are now receiving scorn because they did not wait for the Darwinian imprimatur. Intelligent Design people and creationists (in fact everyone who is not a Darwinist) should take courage from this, jump in and start driving forward ordinary mainstream science, but just make sure they sidestep the attempts to sign them up to that cult.

Does anyone still wonder why I refer to Intelligent Design Creationists as IDiots?

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Estimating the Human Mutation Rate: Biochemical Method

This is the second in a series of posts on human mutation rates and their implication(s). The first one was ...
What Is a Mutation?

There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method.

The biochemical method relies on the well-known fact that the vast majority of mutations are due to errors in DNA replication. Since we know a great deal about the replication complex and the biochemistry of the reactions, we can calculate a mutation rate per DNA replication based on this knowledge. The details are explained in a previous post [Mutation Rates]. I'll give a brief summary here.

The overall error rate of DNA polymerase in the replisome is 10^-8 errors per base pair. Repair enzymes fix 99% of these lesions for an overall error rate of 10^-10 per bp. That means one mutation in every 10 billion base pairs that are replicated.

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies
The human haploid genome is 3.2 × 10⁹ bp. [How Big Is the Human Genome?] [How Much of Our Genome Is Sequenced? ]. That means that on average there are 0.31 mutations introduced every time the genome is replicated. In the male, there are approximately 400 cell divisions between zygote and the production of a sperm cell.¹ This gives a total of about 124 new mutations in every sperm cell. In the female, there are about 30 cell divisions between zygote and the production of egg cells. That's about 9 new mutations in every egg cell.

Adding these together gives us about 133 new mutations in every zygote. Let's round this off to 130. Thus the estimate from the Biochemical Method is ..

130 mutations per generation

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[Image Credit: Wikipedia: Creative Commons Attribution 2.0 Generic license]

1. This depends on the age of the man when he has children. The value used here is approximately the average for a 30 year old man.

Monday's Molecule #200

This is the 200th Monday's Molecule. I started this series back on November 13, 2006. Today's molecule is a repeat of that first one. Let's see if readers in 2013 can do better than those in 2006! The last "Monday's Molecule" was puromycin [Monday's Molecule #199]. The winners were Bell Gunn and River Jiang. River needs to contact me by email to set up a lunch date. I'm going to try and treat all the previous winners this week so if I owe you a lunch you should get in touch right away to collect.

The mystery molecule is an aldohexose. There are 16 different aldohexoses. The structures and names of 8 of them are show below in order to help you out.

This is a tough one. You have to know several carbohydrate naming conventions and you have to understand Fischer projections. Good luck.



Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post 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 comment.)

Read more »

R.S. Bagnall, P. Davoli, C.A.C. Hope edd., The Oasis Papers 6: Proceedings of the Sixth International Conference of the Dakhleh Oasis Project

 ISBN: 9781842175248 | Published by: Oxbow Books | Series: Dakhleh Oasis Project Monograph | Volume: 15 | Year of Publication: 2013 | Language: English 512p,

Table of Contents

General 
Major Archaeological Sites in Kharga Oasis and Some Recent Discoveries by the Supreme Council of Antiquities (Bahgat A. Ibrahim) 
Wanderers in the Desert: The North Kharga Oasis Survey’s Exploration of the Darb ‘Ain Amur (Salima Ikram) 
Demotische und kursivhieratische Ostraka aus Mut al-Kharab (Günter Vittmann) 
Cultural Heritage Management of the Archaeological Resources of the Deserts of Egypt (Sayed Yamani) 

Prehistory 
The Culture of the Oases: Late Neolithic Herders in Farafra, A Matter of Identity (Barbara E. Barich) 
Geomatics Resources for Archaeological Survey in Desert Areas – Some Prospects from Farafra Oasis, Egypt (Barbara E. Barich, Mattia Crespi, Ulisse Fabiani and Giulio Lucarini) 
Beyond the Shale: Pottery and Cultures in the Prehistory of the Egyptian Western Desert (Maria C. Gatto) 
The Gebel Souhan Problem: Local Innovation in the Middle Stone Age? (Maxine R. Kleindienst and Marcia F. Wiseman) 
Early Craftsmen of the Desert. Traces of Predynastic Lithic Technology at Farafra during the Mid-Holocene (Giulio Lucarini) 
Levallois Lithics on a Middle Stone Age Playa: Finds at Bir el-Obeiyid, Northern Farafra Depression, Egypt (Giuseppina Mutri) 
Wadi Sura and the Gilf Kebir National Park: Challenge and chance for archaeology and conservation in Egypt’s south-west (Heiko Riemer and Rudolph Kuper) 
The Khargan Industry Revisited (Marcia F. Wiseman) 
Technique and Content in the Rock Art of the Libyan Fezzan: some Saharan Stereotypes (Daniela Zampetti) 

Pharaonic 
Egyptian Connections with Dakhleh Oasis in the Early Dynastic Period to Dynasty IV: new data from Mut al-Kharab (Colin A. Hope and Amy J. Pettman) 
Epigraphic Evidence from the Dakhleh Oasis in the Late Period (Olaf E. Kaper) 
An Old Kingdom Trading Post at ‘Ain el-Gazzareen, Dakhleh Oasis (Anthony J. Mills) 
The Date of the Occupation of ‘Ain el-Gazzareen based on Ceramic Evidence (Amy J. Pettman) 
Provisions for the Journey: Food Production in the ‘bakery’ area of ‘Ain el-Gazzareen, Dakhleh Oasis (Amy J. Pettman, Ursula Thanheiser and Charles S. Churcher) 

Ptolemaic 
Ptolemaic Period Pottery from Mut al-Kharab, Dakhleh Oasis (James C. R. Gill) 

Roman 
An Agricultural Account from the Gemellos Archive (Giuseppina Azzarello) 
Cemeteries in Dakhleh (Maher Bashendi) 
Amheida 2007–2009: New Results from the Excavations (Paola Davoli) 
Les Nécropoles d’el-Deir (Oasis de Kharga) (Françoise Dunand, Jean-Louis Heim and Roger Lichtenberg) 
Yale University Nadura Temple Project: 2009 Season (David Klotz) 
al-Qasr: the Roman Castrum of Dakhleh Oasis (Paul Kucera) 
Five Roman-Period Tunics from Kellis (Rosanne Livingstone) 
A Remark on the Poll Tax Rate in Kysis (Fabian Reiter) 
Controlling the Borders of the Empire: the distribution of Late-Roman ‘forts’ in the Kharga Oasis (Corinna Rossi) 
Painted Surfaces on Mud Plaster and Three-Dimensional Mud Elements: The Status of Conservation Treatments and Recommendations for Continuing Research (Constance S. Silver) 
The Survey Project at el-Deir, Kharga Oasis: First Results, New Hypotheses (Gaëlle Tallet, Jean-Paul Bravard, Romain Garcier, Stéphanie Guédon and Ashraf Mostapha) 
Amheida: Architectural Conservation and Site Development, 2004–2009 (Nicholas Warner) 
Vine and Acanthus: decorative themes in the wall-paintings of Kellis (Helen Whitehouse) 

Christian 
The Church Complex of ‘Ain el-Gedida, Dakhleh Oasis (Nicola Aravecchia) 
Christianity on Thoth’s Hill (Roger S. Bagnall and Raffaella Cribiore) 
Coins as Tools for Dating the Foundation of the Large East Church at Kellis: problems and a possible solution (Gillian E. Bowen) 
The Church of Dayr Abu Matta and its Associated Structures: an overview of four seasons of excavation (Gillian E. Bowen) 
The Christian Necropolis of el-Deir in the North of Kharga Oasis (Magali Coudert) 
Ceramics from ‘Ain el-Gedida, Dakhleh Oasis: preliminary results (Delphine Dixneuf) 
Coptic Ostraka from Qasr al-Dakhleh (Iain Gardner) 
Naqlun: the Earliest Hermitages (Wlodzimierz Godlewski) 
Contribution of Textiles as Archaeological Artefacts to the Study of the Christian Cemetery of el-Deir (Fleur Letellier-Willemin)

Michael Behe in Toronto: "Evidence of Design from Biology"

Michael Behe gave a talk on the second day of his visit to Toronto (November 16, 2012). This event was sponsored by religious groups even though Intelligent Design has nothing to do with religion—it's strictly a scientific theory.

The video of his first talk is: "What Are the Limits of Darwinism?". Here's his second talk entitled "Evidence of Design from Biology." There were about 100 people in the audience. I'd guess that half of them were supporters and half were skeptics.

Here's the summary of his talk.

• Design is not mystical. Deduced from physical structure of a system
• Everyone agrees aspects of biology appear designed
• There are structural obstacles to Darwinian evolution
• Grand Darwinian claims rest on undisciplined imagination
• Bottom line: Strong evidence for design, little evidence for Darwinism

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Happy Saint Patrick's Day!

One of the cool things about studying your genealogy is that you can find connections to almost everyone. This means you can celebrate dozens of special days. In my case it was easy to find ancestors from England, Scotland, Netherlands, Germany, France, Spain, Poland, Lithuania, Belgium, Ukraine, Russia, United States, and, of course, Ireland.

We will be celebrating St. Patrick's Day today. It's rather hectic keeping up with all the national holidays but somebody has to keep the traditions alive!

Here's my Irish connection.¹ The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

Thomas and Eliza settled in Saskatchewan in 1883 and that's where my grandmother was born. Other ancestors in this line came from the adjacent counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).

My paternal grandfather's father was William Findley Docherty (1852-1920). Many of his ancestors were Irish but his DNA was considerably diluted by contamination from Scots.

That makes me at least one quarter Irish² and entitles me to drink beer and wear green. My children, however, are only one eighth Irish. They aren't allowed to drink beer.


Happy St. Patrick's Day (2011)
Happy St. Patrick's Day (2010)
Happy St. Patrick's Day (2009)
Happy St. Patrick's Day (2008)
Happy St. Patrick's Day (2007)
Niall Nóigiallach - Niall of the Nine Hostages

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1. You don't have to be Irish or have Irish ancestors to celebrate St. Patrick's Day.

2. With the proviso that my Irish great-grandparents are probably descended from English setters who came to Ireland in the 1600s. I usually don't mention this on St. Patrick's day.

The Purpose of "The Scientific Dissent from Darwin" List

A few years ago the IDiots tried to collect a list of credible scientists who supported creationism. They created a statement called "The Scientific Dissent from Darwin." It goes like this ...

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

Only an IDiot would claim that supporters of this statement are also creationists. Many atheist scientists, including me, would agree with the statement. Nevertheless, if you look at the list of people who signed [Scientific Dissent from Darwin List] you'll not find very many evolutionary biologists because we all know that the IDiots will misuse this list.

A few days ago someone named Joshua Youngkin posted to Evolution News & Views (sic) in response to a question about the list. According to Youngkin, the list "is a thorn in the side of those who say there's no scientific debate over whether evolution works in a completely naturalistic fashion."

Why is that? The statement doesn't say anything about god or naturalism. This is exactly the kind of doubletalk you expect from IDiots.

Later on in the post Joshua Youngkin says,

The Dissent from Darwin statement counters and preempts any claim that (1) there is no scientific dissent over how evolution happens, by what means, that is, or that (2) it is unscientific to be skeptical of the proposition that natural selection and random mutation together satisfactorily explain the development of life over time.

There are plenty of ways to "preempt" such a false claim. Reading the scientific literature is one.

The list does serve one important purpose and for that we are truly thankful. It's the best list of Ph.D IDiots that I know of. It's easy to find your local IDiots using a simple word search. For example, I found these names from the University of Toronto: Stephen J. Cheesman Ph.D. Geophysics and Alfred G. Ratz Ph.D. Engineering Physics. Unfortunately, as I pointed out some years ago [I'm not a Darwinist, but I Ain't Signing], neither of these gentlemen are listed in the university phone book and they are not on the University website so we don't know what they are up to these days.

Project Steve with 1249 signatures, is an excellent parody of the creationist list.

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On the Meaning of the Word "Function"

A lot of the debate over ENCODE's publicity campaign concerns the meaning of the word "function." In the summary article published in Nature last September the authors said, "These data enabled us to assign biochemical functions for 80% of the genome ...." (The ENCODE Project Consortium, 2012).

Here's how they describe function.

Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).

What, exactly, do the ENCODE scientists mean? Do they think that junk DNA might contain "functional elements"? If so, that doesn't make a lot of sense, does it?

Ewan Birney tried to address this definitional morass on his blog [ENCODE: My own thoughts] where he says ....

It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e., if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.

That's about as clear as mud.

We all know what the problem is. It's whether all binding sites have a biological function or whether many of them are just noise arising as a property of DNA binding proteins. It's whether all transcripts have a biological function or whether many of those detected by ENCODE are just spurious transcripts or junk RNA. These questions were debated extensively when the ENCODE pilot project was published in 2007. Every ENCODE scientist should know about this problem so you might expect that they would take steps to distinguish between real biological function and nonfunctional noise.

Their definition of "function" is not helpful. In fact, it seems deliberately designed to obfuscate.

Let's see how other scientist interpret the ENCODE results. In a News & Views article published in Nature last September, Joseph R, Ecker (Salk Institute scientist) said ...

One of the more remarkable findings described in the consortium's 'entre&eacute:' paper is that 80% of the genome contains elements linked to biochemical function, dispatching the widely held view that the human genome is mostly 'junk DNA.'

That makes at least one genomics worker who thinks that "biochemical function" and junk DNA are mutually exclusive.

Recently a representative of GENCODE responded to Dan Graur's criticism [On the annotation of functionality in GENCODE (or: our continuing efforts to understand how a television set works)]. This person (JM) says ...

Q1: Does GENCODE believe that 80% of the genome is functional?

As noted, we will only discuss here the portion of the genome that is transcribed. According to the main ENCODE paper, while 80% of the genome appears to have some biological activity, only “62% of genomic bases are reproducibly represented in sequenced long (>200 nucleotides) RNA molecules or GENCODE exons”. In fact, only 5.5% of this transcription overlaps with GENCODE exons. So we have two things here: existing GENCODE models largely based on mRNA / EST evidence, and novel transcripts inferred from RNAseq data. The suggestion, then, is that there is extensive transcription occurring outside of currently annotated GENCODE exons.

There's another scientist who thinks that 80% of the genome has some biological activity in spite of the fact that the ENCODE paper says it has "biochemical function." I don't think "biological activity" is compatible with "junk DNA," but who knows what they think?

Since this person is part of the ENCODE team, we can assume that at least some of the scientists on the team are confused.

The Sanger Institute (Cambridge, UK) was an important player in the ENCODE Consortium. It put out a press release on the day the papers were published [Google Earth of Biomedical Research]. The opening paragraph is ...

The ENCODE Project, today, announces that most of what was previously considered as 'junk DNA' in the human genome is actually functional. The ENCODE Project has found that 80 per cent of the human genome sequence is linked to biological function.

It looks like the Sanger Institute equates "biochemical function" and "biological function" and it looks like neither one is compatible with junk DNA.

I think the ENCODE leaders, including Ewan Birney, knew exactly what they were doing when they defined function. They meant "biological function" even though they equivocated by saying "biochemical function." And they meant for this to be interpreted as "not junk" even though they are attempting to backtrack in the face of criticism.

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The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74. (E. Birney, corresponding author)

Anonymous Nature Editors Respond to ENCODE Criticism

There are now been four papers in the scientific literature criticizing the way ENCODE leaders hyped their data by claiming that most of our genome is functional [see Ford Doolittle's Critique of ENCODE ]. There have been dozens of blog postings on the same topic.

The worst of the papers were published by Nature—this includes the abominable summary that should never have made it past peer review (Encode Consortium, 2012).

The lead editor on the ENCODE story was Brendan Maher and he promoted the idea that the ENCODE results showed that most of our genome has a function [ENCODE: The human encyclopaedia]

The consortium has assigned some sort of function to roughly 80% of the genome, including more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 ‘enhancer’ regions that regulate expression of distant genes.

Read more »

Misconceptions about Random Genetic Drift

Genetic Drift

Evolutionary change that occurs by random sampling of different alleles from one generation to the next. This causes nonadaptive evolutionary change.

Jerry Coyne
"Why Evolution Is True"There seem to be two important themes in the current pedagogical literature on science education. One of them is about student-centered learning—a concept I think we should all adopt. The other is about student misconceptions and how to deal with them. Much of the literature suggests that misconceptions need to be confronted and corrected. They can't be corrected by simply presenting the "correct" information. You need to actually address the misconception and show why it is wrong. This is a form of "teach the controversy" and that's not going to sit well with many American supporters of evolution.

Here's an interesting paper on "Biology Undergraduates’ Misconceptions about Genetic Drift" (Andrews et al., 2012). The abstract covers all the important points. Read more »

Barry Arrington Demonstrates IDiot Logic

A few years ago Barry Arrington came up with this killer argument against evolution [see Question: How Can We Know One Belief Selected for By Evolution is Superior to Another?].

Theist: You say there is no God.
Evolutionary Materialist [EM]: Yes.
Theist: Yet belief in God among many (if not most) humans persists.
EM: I cannot deny that.
Theist: How do you explain that?
EM: Religious belief is an evolutionary adaption.
Theist: But you say religious belief is false.
EM: That’s correct.
Theist: Let me get this straight. According to you, religious belief has at least two characterizes: (1) it is false; and (2) evolution selected for it.
EM [looking a little pale now, because he’s just figured out where this is going]: Correct.
Theist: You believe the Neo-Darwinian Synthesis [NDS] is true.
EM: Of course.
Theist: How do you know your belief in NDS is not another false belief that evolution has selected for?
EM: ___________________

Our materialist friends are invited to fill in the blank.

Read more »

Ford Doolittle's Critique of ENCODE

Ford Doolittle has never been one to shy away from controversy so it's not surprising that he weighs in against the misleading publicity campaign launched by ENCODE leaders last September (Doolittle, 2013). Recall that Ewan Birney and other prominent members of the consortium promoted the idea that our genome contained an extensive array of regulatory elements and that 80% of our genome was functional [Ewan Birney: Genomics' Big Talker] [ENCODE Leader Says that 80% of Our Genome Is Functional] [The ENCODE Data Dump and the Responsibility of Scientists].

This is the fourth paper that's critical of the ENCODE hype. The first was Sean Eddy's paper in Current Biology (Eddy, 2012). The second was a paper by Niu and Jiang (2012), and the third was a paper by Graur et al. (2013). In my experience this is unusual since the critiques are all directed at how the ENCODE Consortium interpreted their data and how they misled the scientific community (and the general public) by exaggerating their results. Those kind of criticisms are common in journal clubs and, certainly, in the blogosphere, but scientific journals generally don't publish them. It's okay to refute the data (as in the arsenic affair) but ideas usually get a free pass no matter how stupid they are.

In this case, the ENCODE Consortium did such a bad job of describing their data that journals had to pay attention. (It helps that much of the criticism is directed at Nature and Science because the other journals want to take down the leaders!)

Read more »

What's Wrong with This Statement?

Read the following statement from the Wikipedia article on the Genetic Code.

... the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code.

What wrong with this statement? Cornelius Hunter says that the statement "... is false—at least from a scientific perspective" [Here is Why the DNA Code is a Problem]. Can you guess why this IDiot would make such a claim?

In contrast, an anonymous source at Uncommon Descent asks, "Does the Genetic Code Bear A Signature of Intelligence?." He/she posts the following abstract ...

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like “signal” in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns display readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

According to Uncommon Descent, the article is written by two scientists. They turn out to be two mathematicians from the Republic of Kazakhstan [The “Wow! signal” of the terrestrial genetic code].

Can you guess why the IDiots would believe such a ridiculous claim?

I wonder if Cornelius Hunter thinks this is science?

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Monday's Molecule #199

The last "Monday's Molecule" was phycoerythrin [Monday's Molecule #198]. The winner was Piotr Gasiorowski.

This week's molecule can do some very bad things to certain cells. You just have to give the common name and briefly explain what it does and how it works.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post 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 comment.)

Read more »

Michael Behe in Toronto: "What Are the Limits of Darwinism?"

Michael Behe was in Toronto a few months ago (November 2012). He gave three talks while he was here. You can read my summaries at: Michael Behe In Toronto: Part 1,
Michael Behe in Toronto: Part 2, and Michael Behe in Toronto: Part 3. (You can also check out My Posts on Michael Behe)

The first talk was quite private and it was not recorded. The second talk, on a Thursday evening, was in one of the main lecture theaters in my building. There were at least 400 people in the audience. This talk was on the "Limits of Darwinism" and it was recorded. You can watch it in the video below.

Read more »