Wednesday, July 31, 2013

The Dark Matter Rises

John Mattick is a Professor and research scientist at the Garvan Institute of Medical Research at the University of New South Wales (Australia).

John Mattick publishes lots of papers. Most of them are directed toward proving that almost all of the human genome is functional. I want to remind you of some of the things that John Mattick has said in the past so you'll be prepared to appreciate my next post [The Junk DNA Controversy: John Mattick Defends Design].

Mattick believes that the Central Dogma means DNA makes RNA makes protein. He believes that scientists in the past took this very literally and discounted the importance of RNA. According to Mattick, scientists in the past believed that genes were the only functional part of the genome and that all genes encoded proteins.

If that sounds familiar it's because there are many IDiots who make the same false claim. Like Mattick, they don't understand the Central Dogma of Molecular Biology and they don't understand the history that they are distorting.

Mattick believes that there is a correlation between the amount of noncoding DNA in a genome and the complexity of the organism. He thinks that the noncoding DNA is responsible for making tons of regulatory RNAs and for regulating expression of the genes. This belief led him to publish a famous figure (left) in Scientific American.

Mattick has many followers. So many, in fact, that the Human Genome Organization (HUGO) recently gave him an award for his contributions to the study of the human genome. Here's the citation.
Theme
Genomes
& Junk DNA
The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”
Let's see what this "true visionary" is saying this year. The first paper is "The dark matter rises: the expanding world of regulatory RNAs" (Clark et al., 2013). Here's the abstract ...
The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.
This is his main theme. Mattick believes that a large percentage of the human genome is devoted to making regulatory RNAs that control development. He believes that the evolution of this complex regulatory network is responsible for the creation of complex organisms like humans, which, incidentally, are the pinnicle of evolution according to the figure shown above.

The second paper I want to highlight focuses on a slightly different theme. It's title is "Understanding the regulatory and transcriptional complexity of the genome through structure." (Mercer and Mattick, 2013). In this paper he emphasizes the role of noncoding DNA in creating a complicated three-dimensional chromatin structure within the nucleus. This structure is important in regulating gene expression in complex organisms. Here's the abstract ...
An expansive functionality and complexity has been ascribed to the majority of the human genome that was unanticipated at the outset of the draft sequence and assembly a decade ago. We are now faced with the challenge of integrating and interpreting this complexity in order to achieve a coherent view of genome biology. We argue that the linear representation of the genome exacerbates this complexity and an understanding of its three-dimensional structure is central to interpreting the regulatory and transcriptional architecture of the genome. Chromatin conformation capture techniques and high-resolution microscopy have afforded an emergent global view of genome structure within the nucleus. Chromosomes fold into complex, territorialized three-dimensional domains in concert with specialized subnuclear bodies that harbor concentrations of transcription and splicing machinery. The signature of these folds is retained within the layered regulatory landscapes annotated by chromatin immunoprecipitation, and we propose that genome contacts are reflected in the organization and expression of interweaved networks of overlapping coding and noncoding transcripts. This pervasive impact of genome structure favors a preeminent role for the nucleoskeleton and RNA in regulating gene expression by organizing these folds and contacts. Accordingly, we propose that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome.
Other posts about John Mattick.

How Not to Do Science
John Mattick on the Importance of Non-coding RNA
John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research
International team cracks mammalian gene control code
Greg Laden Gets Suckered by John Mattick
How Much Junk in the Human Genome?
Genome Size, Complexity, and the C-Value Paradox


Clark, M.B., Choudhary, A., Smith, M.A., Taft, R.J. and Mattick, J.S. (2013) The dark matter rises: the expanding world of regulatory RNAs. Essays in Biochemistry 54:1-16. [doi:10.1042/bse0540001]

Mercer, T.R. and Mattick, J.S. (2013) Understanding the regulatory and transcriptional complexity of the genome through structure. Genome research 23:1081-1088 [doi: 10.1101/gr.156612.113]

Teach the Controversy

I favor a strategy called "Teach the Controversy."1 I think high school teachers should directly address issues that are controversial in society. In science classes they should address and debunk common misconceptions about science.

There doesn't seem to be much of a problem with this idea in Canada but in the United States there is a lot of opposition to the idea. Check out Jerry Coyne's recent post to see what I mean: Once again Larry Moran decries legal battles against creationism.

Let's focus on a specific example. First, we need some background. Many state legislatures in the USA have seriously considered, or passed, so-called Academic Freedom bills. On the surface, these bill look innocuous. They are designed to promote critical thinking in state schools. Part of that process involves challenging and debating controversial science topics. We all know, however, that the real propose is to allow teachers to challenge evolution by teaching alternative "theories" (i.e. creationism).

The state of Louisiana passed the Louisiana Science Education Act in 2008. You can follow the link to a detailed summary of why the legislation is opposed by many scientists and by many scientific and education organizations. So far, attempts to repeal it have failed and no group has been able to mount a successful legal challenge. If this ever gets to court it will soak up thousands of hours of time and effort and it's not clear what the result will be. It would be a disaster if the National Center for Science Education (NCSE) and the American Civil Liberties Union (ACLU) sued the state and lost.

Why not try a different strategy? Here's the text of the Louisiana Science Education Act
Section 1. R.S. 17:285.1 is hereby enacted to read as follows:

§285.1. Science education; development of critical thinking skills

A. This Section shall be known and may be cited as the "Louisiana Science Education Act."

B.(1) The State Board of Elementary and Secondary Education, upon request of a city, parish, or other local public school board, shall allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including, but not limited to, evolution, the origins of life, global warming, and human cloning.

(2) Such assistance shall include support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied, including those enumerated in Paragraph (1) of this Subsection.

C. A teacher shall teach the material presented in the standard textbook supplied by the school system and thereafter may use supplemental textbooks and other instructional materials to help students understand, analyze, critique, and review scientific theories in an objective manner, as permitted by the city, parish, or other local public school board unless otherwise prohibited by the State Board of Elementary and Secondary Education.

D. This Section shall not be construed to promote any religious doctrine, promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.

E. The State Board of Elementary and Secondary Education and each city, parish, or other local public school board shall adopt and promulgate the rules and regulations necessary to implement the provisions of this Section prior to the beginning of the 2008-2009 school year.
Why not find a few high school teachers and support them in an effort to adhere to the law by teaching critical thinking? They could choose a couple of examples of controversial ideas in Louisiana society and address them head-on in their science classes. I suggest two popular ideas that challenge the textbook description of evolution.
  1. The universe was created only 6000 years ago.
  2. Humans were created separately from apes.
The scientific community could support these teachers by preparing "support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied" and by developing lesson planes to cover the material in just a few hours for each topic.

The evidence and lesson plans could be posted online and evolution supporters could publicize the lessons and show how effective it is to teach critical thinking by debunking some popular myths. At first there may be only a few teachers willing to take a stand but hopefully those numbers would grow as more and more teachers realize that they will have solid support from the scientific community.

Even students who aren't in the designated classrooms will become aware of the dangers of teaching the controversy. Maybe state politicians will have second thoughts. They might try and silence the teachers but that would be difficult given that the law specifically encourages teachers to teach the controversy. It would be interesting if they tried to stop the lessons by claiming that those ideas were religious and debunking them was an example of discrimination against religion.

I submit that this might be a far more effective strategy for changing people's minds than fighting another court case.

Please don't argue that those two ideas aren't "science" and should never be discussed in a science classroom. Those ideas are attacks on science and they are certainly part of the controversy about evolution—at least in Louisiana. Moreover, those are exactly the sorts of things that the politicians had in mind when they voted overwhelmingly for this law back in 2008. There's no better way to teach critical thinking than to use specific examples of bad science to show students how to recognize the difference between good science and bad science.

Many people think that teaching the controversy means bringing stupid ideas into the classroom and treating them as if they were respectable alternatives to real science. That's a false assumption. You can just as easily bring stupid ideas into the classroom and teach students why they are stupid ideas. That would be a good thing.


[Image Credit: The images are from Intelligently designed Sarcastic T-shirts. They don't necessarily support my position on this issue but they have cool T-shirts.]

1. I'm perfectly well aware of the fact that Teach the Controversy is a Discovery Institute slogan and ad campaign.

Monday, July 29, 2013

Monday's Molecule #211

Last week's molecule was the the R stereoisomer of ibuprofen [((R)-2-(4-(2-methylpropyl)phenyl)propanoic acid]. The winner was undergraduate Jacob Toth. [Monday's Molecule #210].

Today's molecule is an easy one. All you have to do is give the common name and a brief explanation of its significance.

Email your answers to me at: Monday's Molecule #211. I'll hold off posting your answers for 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.)

Sunday, July 28, 2013

The 25 Richest People Who Ever Lived

This list is biased toward Americans and Englishmen. I'm sure there are many others who deserve to be in the top 25. There are other problems; for example, property values in the middle ages are probably inflated. Nevertheless, it's an interesting list of men (no women). They are ranked by their estimated net worth in 2012 inflation-adjusted American dollars. You can find out more details at: The 25 Richest People Who Ever Lived – Inflation Adjusted.

There don't appear to be any scientists (or philosophers) on the list. Three of my ancestors are on the list (#6, #15, and #16) but I didn't inherit a penny.
  1. Mansa Musa I of Mali (1280-1337): $400 billion
  2. The Rothschild family: $350 billion
  3. John D. Rockefeller (1839-1937): $340 billion
  4. Andrew Carnegie (1835-1919): $310 billion
  5. Tsar Nicholas II of Russia (1868-1918): $300 billion
  6. Mir Osman Ali Khan (1886-1967): $230 billion
  7. William The Conqueror (1028-1087): $229.5 billion
  8. Muammar Gaddafi (1942-2011): $200 billion
  9. Henry Ford (1863-1947): $199 billion
  10. Cornelius Vanderbilt (1794-1877): $185 billion
  11. Alan Rufus (1040-1093): $178.65 billion
  12. Bill Gates (1955 - ): $136 billion
  13. William de Warenne ( -1088) $147.13 billion
  14. John Jacob Astor (176-1848): $121 billion
  15. Richard FitzAlan (1306-1376): $118.6 billion
  16. John of Gaunt (1340-1399): $110 billion
  17. Stephen Girard (1750-1831): $105 billion
  18. Alexander Turney ("A.T.") Stewart (1803-1876): $90 billion
  19. Henry of Grosmont (Duke of Lancaster) (1310-1361): $85.5 billion
  20. Friedrich Weyerhauser (1834-1914): $80 billion
  21. Jay Gould (1836-1892): $71 billion
  22. Carlos Slim Helu (1940- ): $68 billion
  23. Stephen Van Rensselaer (1764-1839): $68 billion
  24. Marshall Field (1834-1906): $66 billion
  25. Samuel ("Sam") Moore Walton (1918-1992): $65 billion
  26. Warren Buffett (1930 - ): $64 billion

My Connection to Geoffrey Chaucer and Medieval Science

One of my ancestors is Katherine de Roet (1349-1403) better known as Katherine Swynford since she married Hugh Swynford. Katherine was the mistress (later wife) of John of Gaunt (1340-1399) and they had several children. I descend from one of them, John Beaufort (1373-1410).1

Katherine's father was Paon de Roet better known as Sir Gilles. He comes from Hainault in Belgium and he served Philippa of Hainault who became the wife of King Edward III of England.

Katherine's sister, also called Philippa (1346-1387) [Philippa Roet] was a prominent member of Queen Philippa's court in England. At first, she was a child companion of the children of Elizabeth of Ulster and the Queen but later on she was a lady-in-waiting. Geoffrey Chaucer became a page in the household of Elizabeth of Ulster in 1357 when he was 14 and Phillipa was 11.

Queen Philippa encouraged them to marry in September 1366. Chaucer and Philippa Roet had two sons and two daughters. The youngest son, Lewis, was born in 1381 and attended Oxford beginning in 1391. Chaucer noticed that his son was interested in science and he wrote A Treatise on the Astrolabe to explain the workings of an astrolabe that he gave him when he was about 10 years old.

A Treatise on the Astrolabe
Geoffrey Chaucer

Lyte Lowys my sone, I aperceyve wel by certeyne evydences thyn abilite to lerne sciences touching nombres and proporciouns; and as wel considre I thy besy praier in special to lerne the tretys of the Astrelabie. Than for as moche as a philosofre saith, "he wrappith him in his frend, that condescendith to the rightfulle praiers of his frend," therfore have I yeven the a suffisant Astrolabie as for oure orizonte, compowned after the latitude of Oxenforde; upon which, by mediacioun of this litel tretys, I purpose to teche the a certein nombre of conclusions aperteynyng to the same instrument.

[Little Lewis my son, I perceive well by certain evidences thine ability to learn sciences touching numbers and proportions; and as well consider I thy constant prayer in special to learn the treatise of the Astrolabe. Than for as much as a philosopher saith, "He wrappth him in his friend, that condescendth to the rightful prayers of his friend", therefore have I given thee a suffisant Astrolabe as for our horizons, compounded after the latitude of Oxford; upon which, by means of this little treatise, I purpose to teach thee a certain number of conclusions pertaining to the same instrument.


[Image credits: Wikipedia: Geoffrey Chaucer, Wikipedia: Chaucer Astrolobe]

1. Almost everyone who has European ancestors will eventually connect to European nobility so there are millions of people who descend from John of Gaunt [see Are You a Descendant of Charlemagne?]. If you know the names of all sixteen of your great-great-grandparents and their dates and places of birth, then chances are high that you can make the connection with only a little effort.

Friday, July 26, 2013

On Beating Dead Horses

I've mentioned this before but it bears repeating. One of my Ph.D. students (Sharon Shtang) wrote her thesis on sequence comparisons and phylogenetic trees. She found a quotation from Emil Zuckerkandl and Linus Pauling in their 1965 review. They were commenting on using amino acid sequences to prove evolution. This seemed at the time to be an example of overkill since evolution was then, and is now, a fact. They said ...
Some beating of dead horses may be ethical, where here and there they display unexpected twitches that look like life.
I was reminded of this while reading Salvador Corova's latest post on Uncommon Descent because he refers to beating dead horses [If not Rupe and Sanford’s presentation (8/6/13), would you believe Wiki? In this case, yes]. I'm not going to make any comments. Read it and weep for the IDiots.
Theme

Mutation
Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian (neutral evolution). When pressed, they’ll say neutral drift is real, but they don’t like it when the dots are connected in a way that demonstrates neutral evolution refutes Darwinism, that there is a contradiction between Dawkins’ vision and neutral evolution! The way Darwinists deal with this violation of the law of non-contradiction is to pretend no contradiction exists. They’ll obfuscate and fog the issue with myriad technical terms and irrelevancies so that the illusion of non-contradiction is protected from public view. Confusion and the illusion of some higher knowledge are their friends, clarity and education of the public are their enemies.

If Dawkins had been faithful to the facts, he wouldn’t have even written The Blind Watchmaker because population genetics precludes his vision of evolution from being reality in anything but his silly Weasel simulations.

There is a simple formula from Wiki that says the rate of new mutations is the rate at which new mutations become features of every member of the population (a process called fixation).

http://en.wikipedia.org/wiki/Fixation_(population_genetics)


The population size is N and the Greek symbol μ (mu) is the mutation rate.

It stands to reason a slightly deleterious mutation is almost neutral, hence, approximately speaking the rate that slightly deleterious mutations become part of every member of the population is on the same order of the slightly deleterious mutation rate. That means if every human is getting 100 dysfunctional mutation per generation, about 100 dysfunctional mutations are getting irreversibly infused into humans every generation (a ratchet so to speak).

But as bad as that is, it’s actually worse in reality. Remember broken bacterial parts in anti-biotic resistance, or blindness in cave fish, or sickle cell anemia? Those are “beneficial” (in the Darwinian sense) mutations, but destructive in the functional sense. So it is actually generous the creationists are modeling the dysfunctional mutations as slightly deleterious (whereas a fair argument might actually model some of the dysfunctional mutations as “beneficial”). So the creationists are cutting Darwinists a lot of slack, and yet, even then the dysfunctional mutations will get fixed (become members of all individuals) in a population! Not to mention, lots of bad may get purged from a population only to get replaced with new generations of bad....

But obvious math is something Darwinism hates dealing with! The above equation should be painful evidence against evolution being some process of increasing complexity from a primordial virus to incredible minds like Newton or Einstein. Darwinist won’t come to terms with it, they won’t come to terms with even a computer simulation based on population genetic models. Oh well! But anyway, Christopher Rupe and John Sanford will be presenting the results of a computer simulation that illustrates the above equation. It’s sort of like beating a dead horse or beating living puppies. It’s not very sporting, but Darwinists keep propping up that dead horse for creationists to keep beating.


Zuckerkandl, E. and Pauling, L. (1965) in EVOLVING GENES AND PROTEINS, V. Bryson and H.J. Vogel eds. Academic Press, New York NY USA

Should Trinity Western University Law School Be Granted Accreditation?

Trinity Western University is located in Langley, British Columbia, Canada. It wants to have a Law School so it has applied for accreditation from the Federation of Law Societies of Canada. Many people are opposed, including The Globe and Mail: Trinity Western should emulate its U.S. equivalents.
The Federation of Law Societies of Canada should not accredit a new law school at Trinity Western University. Doing otherwise would be to endorse the university’s discrimination against gays and lesbians. The FLSC should also use this occasion to follow the lead of its American counterpart and adopt anti-discrimination standards for all law schools seeking accreditation.
What's the problem? The problem is that Trinity Western University is a Christian college that requires that all students and staff adhere to certain "Christian" principles. Here's what they say in their Community Covenant.
This covenant applies to all members of the TWU community, that is, administrators, faculty and staff employed by TWU and its affiliates, and students enrolled at TWU or any affiliate program. Unless specifically stated otherwise, expectations of this covenant apply to both on and off TWU’s campus and extension sites. Sincerely embracing every part of this covenant is a requirement for employment. Employees who sign this covenant also commit themselves to abide by TWU Employment Policies. TWU welcomes all students who qualify for admission, recognizing that not all affirm the theological views that are vital to the University’s Christian identity. Students sign this covenant with the commitment to abide by the expectations contained within the Community Covenant, and by campus policies published in the Academic Calendar and Student Handbook.

...

People face significant challenges in practicing biblical sexual health within a highly sexualized culture. A biblical view of sexuality holds that a person’s decisions regarding his or her body are physically, spiritually and emotionally inseparable. Such decisions affect a person’s ability to live out God’s intention for wholeness in relationship to God, to one’s (future) spouse, to others in the community, and to oneself. Further, according to the Bible, sexual intimacy is reserved for marriage between one man and one woman, and within that marriage bond it is God’s intention that it be enjoyed as a means for marital intimacy and procreation. Honouring and upholding these principles, members of the TWU community strive for purity of thought and relationship, respectful modesty, personal responsibility for actions taken, and avoidance of contexts where temptation to compromise would be particularly strong.
In other words, gays and lesbians are not going to be welcome at the Law School.

It seems pretty straightforward to me. As Veronica Abbas points out "FLSC doesn’t need to need to emulate or follow the precedents of any other countries1 law schools, it should insist that Trinity Western University follow the Canadian Human Rights Act and BC Human Rights Code as a prerequisite for accreditation" [No Gays Need Apply].


1. If I were interested in correcting her spelling and grammar, I might suggest "country's"—but I would never do that, it would get me in big trouble!

Thursday, July 25, 2013

Get a Job: Dallas, Texas (USA)

The Chair of my department1 asked me to post this job advertisement in case any biochemists might be interested. It's a challenging position in Dallas, Texas. You'll have plenty of opportunity to investigate some of the weirdest subjects in all of biology. All you really need is an inquisitive mind—with a few minor restrictions [Wanted: Young Creation Scientists].
ICR, together with the rest of the creation science movement, has made great strides in the last 40 years. In many areas, the superiority of the creation worldview has been clearly demonstrated. Even now, ICR is making exciting discoveries in the fields of biology and geology, and we have started new research initiatives in the field of astronomy. However, there is much work that still needs to be done, and this work is hindered by a lack of trained scientists.

Therefore, we appeal to any Bible-believing young person with an interest in science—have you considered cultivating that science interest for the glory of God?

Many young people choose careers for all the wrong reasons (e.g., maybe a college major is “easy” or they can earn a lot of money). Yet some choices in this area can have negative consequences later in life.What good is it to earn a large salary if your job is unfulfilling? Is it worth it to major in an easy field if you ultimately get a job that you dislike? Little wonder that so many adults are eager to retire from the workforce—they hate their jobs!

How much better to choose a career path that will bring ultimate fulfillment, a decision inspired by a God-given desire to work in a field that will bring glory to the Creator. Young Christian, if God has given you a desire to serve Him in a particular area, then consider His promptings. Maybe He is leading you to serve Him in the field of science. It may involve short-term sacrifice, but God’s best often requires hard work.

If you have an interest in science, then pursue it. An aptitude and a genuine love for science is a rare gift—maybe you can be the one to make a startling discovery or a life-changing advancement in the field. Maybe history will be different because of you. Perhaps you can be the one to finally break the evolutionary monopoly on our institutions of higher learning.

Of course, not everyone has an interest in science. God has given us all different gifts (1 Corinthians 12:4-7) and called us to different areas of service. But Christian young people might consider the challenge to seek God’s wisdom about their future, to consider His direction when they are making their career choices.

For those who do have an interest in science, we wish to offer a few words of advice. Work hard to get the best possible grades and push yourself to truly understand the material. When choosing a school, choose one with a rigorous academic program and a research program that truly interests you. Although you should not be dishonest about what you believe, it’s probably prudent to not draw attention to your creationist beliefs while you are a student, particularly if you are in a field that directly touches upon the origins controversy (such as paleontology, biology, or geology).

Given the increasing anti-Christian sentiment in society and the academic persecution in the secular universities, there may very well come a day when it will no longer be possible for a Bible-believing Christian to get an advanced degree in the natural sciences. Academically gifted young Christians should therefore “redeem the time” (Ephesians 5:16) before that door of opportunity closes.
They don't say how many letters of reference they need. They also don't mention salary. Something in the range of $100,000 - $120,000 would be typical for real scientists at a good school in Texas. ICR probably has to pay more in order to get the very best candidates.

Start-up funds are negotiable but you should probably ask for one million dollars to set up a decent lab. That's about the minimum you're going to need since your chances of getting NIH or NSF funding are pretty slim.


1. He has a great sense of humor. I'm not sure if he wants to be identified by name on this blog but you can find him on our website under Justin Nodwell, Chair.

Every non-lethal genome position is variable in the human population

Melissa Wilson Sayres blogs at mathbionerd and Panda's Thumb. A recent post on Panda's Thumb address a tweet from Daniel Wegmann where he said "Every non-lethal genome position is variable in the human population."

She asks "Is this true?" and proceeds to show that it is [How many mutations?]. She assumes that the human mutation rate is 1.2 × 10-8 per sit per generation. Multiply this by 7.16 billion people on the planet and you get an average of 86 mutations at every single base pair in the human genome.1

Many of these mutations will be deleterious and they will be quickly eliminated from the population if they are lethal or cause severe problems. Some moderately and slightly deleterious mutations will be present in the population because they haven't yet been eliminated by negative selection. (Some will have no effect if they are present in only one copy of your diploid genome.)

To a first approximation, the statement is pretty accurate. If it's true that most of our genome is junk then the nucleotide sequence is not important.2 As we sequence more and more genomes we should see heterogeneity at 90% of the base pairs in the genome. We haven't reached this sort of coverage but all available evidence is consistent with the idea that most positions can be variable.


1 I prefer a larger mutation rate of 100 new mutations per generation for a total of 112 mutations at every site.

2. This doesn't rule out functions that are not sequence-specific. Such functions are known to exist but there are no reasonable hypotheses that justify such functions for most of the genome.

David Klinghoffer Asks a Serious Question?

Well, maybe not really serious. His latest post on Evolution News & Views (sic) is about something called "Darwinian censorship" ["Shut Up," They Said: On the Medved Show, John West Discusses Darwinian Culture of Censorship].

At the end, he asks ...
When did you last hear of a Darwinist willing to seriously entertain -- not merely condemn and shout down -- counterarguments. The most frequently employed argument in the Darwinian arsenal at the moment is "Shut up."
It seems to me that real scientists and philosophers have spent a considerable amount of time addressing the claims of Intelligent Design Creationism. I could even argue that they have spent too much time given that IDiots rarely pay attention.

In my own area of expertise, I've addressed many of the claims made in Darwin's Black Box, The Edge of Evolution, Icons of Evolution, The Myth of Junk DNA, Science & Human Origins, and Signature in the Cell. I've also discussed dozens of blog posts over the years.

And I'm not alone. There are hundreds of articles and posts by dozens of scientists and philosophers. David Klinghoffer's question is ridiculous. Perhaps he's confused because he demands "seriously entertain" and he's disappointed when we seriously entertain their arguments and conclude that they are silly. Perhaps he will only accept that we have "seriously entertained" their arguments when we agree with them? That wouldn't surprise me, it's perfectly consistent with creationist logic.


Tuesday, July 23, 2013

IDiots Don't Understand Punctuated Equilibria

Intelligent Design Creationism is a movement dedicated to discrediting evolution and attacking the rational explanation of nature.1 The evidence is in the books and blogs and the propaganda distributed to local school boards and state legislators. The attack on science and scientists makes up about 99% of their activities.

Given their dedication to disproving evolution, you'd think that the IDiots must at least understand it. Maybe not all of them—because there are some really, really, stupid IDiots—but certainly some of the most prominent IDiots should know what they're talking about? Right? Doesn't that seem reasonable?

The facts say otherwise. Off hand, I can't think of a single IDiot who has an adequate understanding of the science they attack. Believe me, I've tried harder than most to find an intelligent believer.

Dan Dennett vs. Andrew Brown

I remember meeting Andrew Brown in a London pub seven years ago. He didn't like the New Atheists then and he still doesn't like them. I remember struggling to understand his accommodationist position back in 2006 and failing completely. At the time I attributed it to the beverages we were consuming but later on as I read his articles—when we were both sober—I realized that his position made no sense.

Andrew Brown sat down with Dan Dennett to discuss "Do the New Atheists have any new ideas?.
Andrew Brown challenges philosopher and atheist Daniel Dennett to convince him that the New Atheists have new ideas – and that they have really changed the face of belief in America. Dennett, one of the original 'four horsemen' of new atheism (along with Richard Dawkins, Sam Harris and Christopher Hitchens), has argued that belief in God is not merely mistaken, but dangerous.
Watch the short video and judge for yourself whether Andrew Brown is making sense.



[Hat Tip: Jerry Coyne]

Ugly Americans

I don't mean to pick on PZ Myers—he's just one of many seemingly intelligent people who think that the American system of government is far superior to the governments of countries like the United Kingdom, Japan, Canada, Australia, Jordan, Spain, Sweden, Malaysia, Belgium, the Netherlands, Norway, and Denmark.

Here's what he posted today [My deepest regrets to the people of the United Kingdom ] ...
Apparently, your antiquated monarchy is going to continue, and the birth of a child of extraordinary privilege warrants far more attention than the birth of thousands who will live in poverty. I hope you get over it soon, and I hope it doesn’t infect my country; despite fighting a revolution to get out from under a king, there are a lot of conservatives with a bizarre sentimental attachment to the idea of a hereditary aristocracy.
There's a certain irony in this statement since Americans are fond of celebrating babies born into extraordinary privilege, especially if they are movie stars. Furthermore, the percentage of children born into poverty in the USA exceeds that of many of the European monarchies. I'm reminded of pots and kettles.

But, more importantly, the condescending attitude of superiority is totally unjustified. The UK is a democracy with a parliamentary system of government and a ceremonial Head of State who happens to be a monarch. It's a system of government that is vastly superior to the American system, in my opinion. The people of the United Kingdom (and all other democratic monarchies) are perfectly capable of abolishing the monarchy if they choose. The fact that they haven't must mean that they like it that way.1 Why can't Americans respect that? They certainly demand that the rest of the world respect their choices!

Why do Americans have so much trouble seeing the world as non-Americans see it?


1. Of course there are many citizens of monarchies who wish to abolish the monarchy. You can be sure that quite a few of them will show up in the comments below.

Monday, July 22, 2013

Donald Prothero Reviews Darwin's Doubt

Donald Prothero is a paleontologist. He has reviewed Darwin's Doubt [ Stephen Meyer's Fumbling Bumbling Cambrian Amateur Follies]. The reason why this is important is because the IDiots want a "real expert" to review the book [see IDiot Ironly.

Well, they got their wish. It's a long, detained review but here's the fun part.
The entire literature of creationism (and of its recent offspring, "intelligent design" creationism) works entirely on that principle: they don't like any science that disagrees with their view of religion, so they pick tiny bits out of context that seem to support what they want to believe, and cherry-pick individual cases which fits their bias. In their writings, they are legendary for "quote-mining": taking a quote out of context to mean the exact opposite of what the author clearly intended (sometimes unintentionally, but often deliberately and maliciously). They either cannot understand the scientific meaning of many fields from genetics to paleontology to geochronology, or their bias filters out all but tiny bits of a research subject that seems to comfort them, and they ignore all the rest.

Another common tactic of creationists is credential mongering. They love to flaunt their Ph.D.'s on their book covers, giving the uninitiated the impression that they are all-purpose experts in every topic. As anyone who has earned a Ph.D. knows, the opposite is true: the doctoral degree forces you to focus on one narrow research problem for a long time, so you tend to lose your breadth of training in other sciences. Nevertheless, they flaunt their doctorates in hydrology or biochemistry, then talk about paleontology or geochronology, subjects they have zero qualification to discuss. Their Ph.D. is only relevant in the field where they have specialized training. It's comparable to asking a Ph.D. to fix your car or write a symphony--they may be smart, but they don't have the appropriate specialized training to do a competent job based on their Ph.D. alone.

Stephen Meyer's first demonstration of these biases was his atrociously incompetent book Signature in the Cell (2009, HarperOne), which was universally lambasted by molecular biologists as an amateurish effort by someone with no firsthand training or research experience in molecular biology. (Meyer's Ph.D. is in history of science, and his undergrad degree is in geophysics, which give him absolutely no background to talk about molecular evolution). Undaunted by this debacle, Meyer now blunders into another field in which he has no research experience or advanced training: my own profession, paleontology. I can now report that he's just as incompetent in my field as he was in molecular biology. Almost every page of this book is riddled by errors of fact or interpretation that could only result from someone writing in a subject way over his head, abetted by the creationist tendency to pluck facts out of context and get their meaning completely backwards. But as one of the few people in the entire creationist movement who has actually taken a few geology classes (but apparently no paleontology classes), he is their "expert" in this area, and is happy to mislead the creationist audience that knows no science at all with his slick but completely false understanding of the subject.


Stop Taking Vitamin Supplements!

Here's a post for all my friends and acquaintances who think they have to load up on vitamin supplements ever day. You don't need them (unless you are ill or pregnant).

If you think you do, then chances are you've fallen victim to one of the biggest scams of modern times. It's not much different than the pitches made by snake oil salesmen over one hundred years ago. There are people making big money by convincing gullible citizens that they have vitamin deficiencies. Some of those people are doctors and many of the enablers are family physicians who don't know the scientific evidence behind vitamin supplements.

"There's a sucker born every minute."

David Hannum
(frequently attributed to P.T. Barnum)
The Atlantic has published a nice summary of the current evidence: The Vitamin Myth: Why We Think We Need Supplements. Most of the article is about Linus Pauling and why he was spectacularly wrong about vitamin supplements. Here's the bottom line ...
On October 10, 2011, researchers from the University of Minnesota found that women who took supplemental multivitamins died at rates higher than those who didn't. Two days later, researchers from the Cleveland Clinic found that men who took vitamin E had an increased risk of prostate cancer. "It's been a tough week for vitamins," said Carrie Gann of ABC News.

These findings weren't new. Seven previous studies had already shown that vitamins increased the risk of cancer and heart disease and shortened lives. Still, in 2012, more than half of all Americans took some form of vitamin supplements.
I'm not convinced that moderate amounts of vitamin supplements will actually cause you much harm—the jury's still out on that IMHO. However, it's now abundantly clear that, for the average healthy person, spending money on vitamin supplements is no different that flushing that money down the toilet, which, coincidentally, is where most of the vitamins you take will eventually end up.

See also: What Kind of People Take Vitamins?.


Re-learning Russian

Ms. Sandwalk and I are going to be in St. Petersburg (Russia) in a few weeks. We plan on spending four hours in the building on the right (and adjacent buildings) although I'm told that's not nearly enough time.

I'm trying to remember my Russian. I last studied it in high school 50 years ago. We've been watching videos of the main tourist spots in St. Petersburg and I can usually figure out what the signs are saying. For example, it was pretty easy to recognize the sign below. In fact, most of you could probably figure it out even if you haven't taken Russian.

Here's the problem. The language in most Western European cities is quite casual compared to the way it was in the past. A typical greeting might be similar to "hi" instead of "How are you?" The comparable words in Russian are Привет and Здравствуйте. Which one is more appropriate in Russia today? And which pronunciation of Здравствуйте should I use?

Similarly, I was taught to say Как вы поживаете (How are you?) but that's a very formal phrase. I get the impression that it's now thought to be archaic and you can easily skip the pronoun by saying Как поживаете. Can you get away with addressing a stranger using the informal first person version of "you," e.g. Как поживаешь?


Monday's Molecule #210

Last week's molecule was the "go" conformation of the leader sequence in the E. coli trp operon. The winners were Rosie Redfield and Quyen Huynh. [Monday's Molecule #209].

Today's molecule isn't very complicated but it has a big effect. You need to be very specific in identifying the exact molecule shown in the figure. I won't accept answers that are ambiguous.

Email your answers to me at: Monday's Molecule #210. I'll hold off posting your answers 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 email message.)

Sunday, July 21, 2013

The Many Faces of Sal Cordova

The IDiots are getting all excited about Nick Matzke because he dared to criticize Darwin's Doubt, a book about evolution written by a philosopher.

The latest post is by Salvador Cordova (scordova) on Uncommon Descent [Two-faced Nick Matzke].

I don't think I can do full justice to the stupidity in this post, you have to read it yourself. Here's the gist ...

Matzke said, quite correctly, that phylogenetic methods can only detect sister groups, not ancestors. This is pretty obvious in the case of sequences because, in most cases, we don't have access to DNA or proteins from extinct ancestors.

Salvador Cordova thinks he was the first one to realize this ...
Not much difference between what Matzke said and I said! I’ve been telling him that since 2006, and now he finally acknowledges it publicly.
Now that's good for a laugh at the expense of IDiots but it gets even funnier. The IDiots think that the absence of living ancestors proves that god(s) created modern species.
I’ve said that it was creationists (like Linnaeus) before Darwin’s time who lumped humans along with the primates, and the primates along with the mammals, etc. The creationists perceived the “sister groups” with no physical ancestor (which suggests the “parent” was an idea in the mind of God, not a physical common ancestor).

The reason Darwinists have all these phylogenetic conflicts is that the ancestors which would resolve all the conflicts are the very ones they will not admit a priori because those ancestors are conceptual, not physical, and conceptual ancestors are anathema to Darwinsits because conceptual ancestors imply ID.
Like I said, you have to read the whole thing ... if you can stomach it.

I wonder why we call them IDiots?


Bill Maher Shows Us that "Smart" People Can Believe Really Stupid Things

Bill Maher thinks he's a smart person ... maybe even an intellectual. Here's a video of him attacking smart people who believe really stupid things. It drips with sarcasm and mockery. At the end of the video you wonder how in the world people could be so stupid. Maher is upset about the resurgence of the "smart-stupid person." One of his targets is a former Prime Minister of Canada.

Hermant Mehta liked this video [Bill Maher Goes After Dr. Eben Alexander and Other Brilliant Scholars Who Believe in Complete Nonsense].


Speaking of smart-stupid people. Here's a video of Bill Maher talking complete nonsense about vaccines. He is corrected by a really smart person, Bill Frist. This is an example of irony and an example of hypocrisy. The hypocrisy is worse than the irony.

Saturday, July 20, 2013

IDiot Irony

Sometimes I really wonder what goes on at the Discovery Institute.

As most of you know by now, Stephen Meyer has written a new anti-evolution book where he criticizes the expert scientific opinion on the Cambrian Explosion. He says that the experts are all wrong and the evidence shows that evolution is impossible. The only reasonable alternative is that god(s) made the primitive animals. Meyer has an undergraduate degree in physics and earth science (1981) and got a Ph.D. in history and philosophy of science ten years later (1991). He is not a scientist and he is not an expert on evolution.

Casey Luskin has a Master's degree in earth sciences but later on he got a law degree and he is primarliy a lawyer. He is not a scientist and he is not an expert on evolution.

David Klinghoffer is a writer. He is not a scientist and he is not an expert on evolution.

Nick Matzke is a graduate student who is finishing up his Ph.D. in evolutionary biology. He is a scientist and he is an expert on evolution. He is also an expert on Intelligent Design Creationism.

Nick Matzke wrote a long review of Darwin's Doubt—a book written by a philosopher [Meyer’s Hopeless Monster, Part II].

Casey Luskin, a lawyer, took it upon himself to critique Matzke's review [How "Sudden" Was the Cambrian Explosion? Nick Matzke Misreads Stephen Meyer and the Paleontological Literature; New Yorker Recycles Misrepresentation]. Luskin says,
Since Matzke published his review, The New Yorker reviewed Meyer's book. Gareth Cook, the science writer who wrote the piece, relied heavily on Matzke's critical evaluation, even though Matzke is a graduate student and not an established Cambrian expert. Cook uncritically recycled Matzke's claim that the Cambrian explosion took "many tens of millions of years," ...
Do you see the irony? Meyer is a philosopher and Luskin is a lawyer but poor old Nick is just a graduate student about to get a Ph.D. in evolutionary biology. Matzke is not an established Cambrian expert. Neither are Meyer or Luskin but that doesn't seem to stop them from criticizing Matzke and all other evolutionary biologists and all paleontologists.1

David Klinghoffer just can't wait to contribute his two cents. Klinghoffer isn't a scientist and he certainly isn't an expert on paleontology but that doesn't mean he can't have an opinion [Regarding Matzke, Coyne, and Darwin's Doubt, a Reader Asks].
That is a good question. Casey Luskin has already demonstrated what a non-paleontologist Matzke is.
How could non-scientist Klinghoffer possibly know whether lawyer Casey Luskin had made a good case against evolutionary biologist Nick Matzke? Does Klinhoffer realize that Luskin is a lawyer, not a paleontologist?

Do you wonder why we call them IDiots?


1. My irony meter survived but it was touch-and-go for a minute or two.

Can You Name These Famous People?

I was cleaning up my files and I came across this photo from seven years ago. It's one of those vanity photos1 where I try to impress you by having my picture taken with famous people.

Can you name all the people in the photo (hint, I'm the one on the right). You're not allowed to guess if you are one of the people in the photo.

Are you impressed? (You should be.)


1. That's what Jerry Coyne calls them

Friday, July 19, 2013

Speaking of Trees

My friends and colleagues, David Isenman and Jacqueline Segall, used to have a big tree in their back yard. On Monday July 8th it rained ... a lot. The ground became very soggy and the tree tipped over.

So much for the life of this tree. They need a new shed.



What Is Humanism?

What the heck is humanism? The short answer is ... I have no idea.

If someone tells me they're a humanist then I can guess that they have some kind of ethical standards that have nothing to do with religion but that's about all I can guess. They might as well have told me that they are an atheist and leave it at that.

Are humanists socialists? Do they all favor socialized medicine and support unions? Do they oppose the death penalty? Are they in favor of gun control and abortion on demand? Do humanists oppose the American war in Afghanistan? Did they support the invasion of Iraq?

Are humanists willing to vote for a Republican or a Conservative? How about a Communist? Do all humanists think gay marriage should be legal? Would they legalize prostitution and pornography? Would they legalize drugs like cocaine and marijuana? How do they feel about euthanasia?

Do humanists support a public school system or are some in favor of vouchers and private schools? Do they all have the same position on immigration? on welfare?

I don't know the answer to any of these questions. I don't know what it means to be a humanist.

Hermant Mehta thinks that Humanism tells us what he believes. Watch this video to see what that means.


Still confused? Go to the American Humanist Association website and you'll be even more confused. Read the Humanist Manifesto and the essays by Fred Edwords. They don't answer any of the questions I asked.


How to Build a Research Institute


The Francis Crick Institute is under construction in London (UK). When I first heard about this I thought that it would be a wonderful place for theoretical biologists—a sort of Institute for Advanced Study for biologists. That would be in keeping with the career of Francis Crick. It's also something that sorely needed in the 21st century because most biology has degenerated into data collection and mining with little attention to ideas and concepts.

Alas, the director, Paul Nurse, had other ideas. He wanted to create "a world-leading centre of biomedical research and innovation." In other words, translation research.

Paul Nurse and two research directors (Richard Treisman and Jim Smith) wrote an editorial in a recent issue of Science [Building Better Institutions]. They take it as a given that what Great Britain needs is a research institute that concentrates on medical research. They also believe that mixing scientists, clinicians, and representatives of the pharmaceutical industry will lead to better results. You better throw in a few physical scientists for good measure because physical scientists have good ideas.
Despite the recent growth in scientific knowledge, conventional discipline-based methods have not been suffi ciently effective at developing new understanding and treatments. Researchers need to be encouraged to identify important questions and tackle them with multidisciplinary approaches. Contemporary biomedical research has to integrate biological, nonbiological, and clinical disciplines, and its application requires interactions with hospital and commercial partners. This can be facilitated by research institutions with an environment that supports strong interdisciplinary interactions between scientists: a place where laboratory biologists are encouraged to collaborate with clinical researchers to understand the medical implications of their work, with pharmaceutical companies for the translation of discoveries into treatments, and with physical scientists to expand their thinking and repertoire of experimental approaches. Such an institution must be continually open to new ideas and permeable to interactions with outside researchers and organizations.
We've been doing exactly that at our hospital research institutes here at the University of Toronto. The industrial relationship has been helped by something we call the MaRS Discovery District. The experiment has been running for over a decade and, as I'm sure you all know, it has been hugely successful. Toronto has been churning out new medical discoveries on a daily basis. (Not!)

The Francis Crick Institute will support young investigators because scientists at the beginning of their career have such a tremendous track record of creativity and originality. (?) In fact, the new institute believes so strongly in young investigator that 80 out of 120 positions will be set aside for them. But what happens when they reach their mid-forties?
These appointments will be of up to 12 years, supported by the Crick's funding partners (the Medical Research Council, Cancer Research UK, and the Wellcome Trust). Group leaders will then leave the institute to establish a research group elsewhere; the aim is to give researchers who are effective and remain in the United Kingdom a transition package to support their moves, creating a thriving network of highly trained researchers.
Science is a risky business so every year there will likely be three or four investigators whose time is up but whose scientific output is just average. What happens when they're tossed out of the institute?

Does anyone think this is a good idea?


What Should We Teach About the "Tree of Life"?

As most of you already know, I think the Three Domain Hypothesis is dead. The history of life is better explained as a net with rampant transfer of genes between species [The Web of Life]. This idea has been widely promoted by Ford Doolittle.

The debate over the tree of life has implications concerning the distinction between "prokaryote" and "eukaryote." I was checking some recent papers and came across one by Doolittle and Zhaxybayeva (2013) that seems particularly relevant. They discuss the evidence for and against the division of life into three domains and the attempt by Norm Pace to band the word "prokaryote."

The authors point out, once again, that eukaryotic genes are most closely related to genes from cyanobacteria, proteobacteria, and archaebacteria, in that order. The majority, by far, have their closest homologs in bacteria, not archaebacteria. The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium plus genes transferred from mitochondria and chloroplast to the nuclear genome.

Thursday, July 18, 2013

The Largest Prokaryotic Genomes

Some bacterial genomes are quite large. A few are larger than the smallest eukaryotic genomes.

Many species of cyanobacteria are complex, multicellular organisms [Multicellular Bacteria]. Those species tend to have large genomes.

Recently Degan et al. (2013) sequenced the genomes of six new cyanobacteria species and one of them turns out to have a large genome.1 (see Contradictory Phylogenies for Cyanobacteria for more information on that paper.) The species is Scytonema hofmanni and its genome is 12,073,012 bp in size. It has 12,356 potential protein-coding genes. If all of them are correctly identified then the total, counting non-protein-coding genes, is likely to be 12,500 genes. That's a record for prokaryotes.

Half of these genes are only found in Scytonema and that's very strange.

There are bacteria with larger genomes, notably the soil bacterium Ktedonobacter racemifer with a genome size of 13,661,586 bp.

For comparison, the genome of the yeast, Saccharomyces cerevisiae, is 12,156,677 bp in size and it has 6,200 genes.


Photo Credit: Scytonema hofmanni from cyanobacteria slides.

1. Some of you might be under the impression that I give a shit about Norm Pace and his attempt to banish the word "prokaryote" (Pace, 2009). Don't bother to try and convince me because it requires that I accept the false Three Domain Hypothesis and that ain't gonna happen.

Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
[doi: 10.1093/gbe/evs117]

Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]

Contradictory Phylogenies for Cyanobacteria

The cyanobacteria are interesting for a number of reasons. They have a complex photosynthesis pathway with two separate phostosystems and an oxygen evolving complex. That means they can use water as an electron donor and NADP as an electron acceptor.

Cyanobacteria probably played an important role in creating an atmosphere with significant levels of oxygen but, contrary to some speculation, they almost certainly arose fairly late in the history of life (i.e. after 500 million years). Cyanobacteria make up a significant proportion of life in the ocean. Primitive cyanobacteria gave rise to chloroplasts in modern plants and algae.

The Shortest Distance ....

I have many pet peeves. One of them concerns the people who build paths and walkways. If you're going to spend a lot of money constructing fancy walkways, then it makes sense to put a little thought into where you're going to put them. As a general rule, you should put the walkway where people are going to walk.

A few years ago (2008), the University of Toronto spent a million dollars on constructing new pathways throughout the downtown campus. The new paths mostly followed the old paths but there were places where that didn't make sense. As I reported back then [If you build it, will they follow?], the old path didn't line up with the new ramp to my building (see photo below). The guys building the path agreed with me that the placement of the walkway made no sense but they were overruled by their supervisor who insisted that the alignment wasn't a problem. People would stay on the new walkway and they would be encouraged to do so by strategic placement of a big rock.



Can you guess what happened? That ramp is now the main entrance to my building for people coming up from the subway exit. Will they follow the path, taking a sharp right turn then a sharp left turn or will they cut straight across the grass making as much of a mess as before the new walkway was constructed?

Here's the result ...


Isn't that ridiculous? Just as predicted, people take the shortest distance between two points and if that means walking over the grass and making an ugly mess, then so be it. What's the point of spending a ton of money to make the campus look nice if this is the result?


Monday, July 15, 2013

Evidence for Intelligent Design

Remember how the IDiots are always trying to tell us that their movement is scientific? It's all about scientific evidence for design.

The facts say otherwise. Almost all of their arguments are based on "evidence" against evolution and on trashing scientists, especially Darwin. Much of their opposition has nothing to do with scientific evidence of design; instead, it's directed at materialism and atheism and other views that they see as an integral part of something called "Darwinism."

Let's see how bizarre this can get. Friedrich Nietzsche ("God is dead") is hardly someone who the IDiots respect for his philosophical view. But that doesn't matter as long as he said something bad about Charles Darwin [Nietzsche, possibly the Nazis’ favourite well-known philosopher, criticized Darwinism on aesthetic grounds].

But, wait a minute. If Nietzsche was a favorite of the Nazis then Darwin must have been opposed to Nazism because Nazi Neitsche criticized natural selection. I'm confused. What does this have to do with evidence of design?


How the IDiots View Genome Research

It's safe to say that a majority of knowledgeable scientists now agree that the most of our genome is junk. This is bad news for Intelligent Design Creationism because they have staked their credibility on the idea that if the DNA is present is must be the product of god(s) the intelligent designer and it must be there for a reason.

One of the latest posts on Evolution News & Views (sic) emphasizes this point [More Clues that Intergenic DNA Is Functional]. Its author doesn't identify herself/himself. The point of the post is to cherry-pick a couple of papers from the scientific literature, including the horrible paper by Hangauer et al. (2013) [see How to Make a Scientific Argument ].

Jenny McCarthy Will Be the New Co-Host of The View

You all remember Jenny McCarthy, right? She's the person who urges parents not to vaccinate their children, prompting formation of the Jenny McCarthy body count.

Sandwalk readers might recall that Jenny McCarthy was scheduled to appear at an Ottawa fund raising event last February until CFI Canada and the Ottawa Skeptics forced the organizers to dump her [Jenny McCarthy Dumped].

Now she's been officially named co-host of The View. What in the world was ABC thinking?

I have sent a complaint to ABC. Here's a convenient webpage: contact us.


Hat Tip: Friendly Atheist.

Monday's Molecule #209

Last week's molecule was depicted on a stamp honoring Gerty Cori. It was supposed to be the "Cori ester" (glucose 1-phosphate) but the image shown on the stamp is not correct. Nobody recognized that so there was no winner last week [Monday's Molecule #208].

Today's molecule is a very famous RNA with secondary structure. Do you recognize it without BLASTing the sequence?

Email your answers to me at: Monday's Molecule #209. I'll hold off posting your answers 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 email message.)

Sunday, July 14, 2013

Happy Bastille Day!

On July 14, 1789 a bunch of French citizens stormed the Bastille and liberated a handful of political prisoners [Bastille Day]. It marks the beginning of the French Revolution.

One of Ms. Sandwalk's ancestors is William Playfair, inventor of pie charts and histograms [Bar Graphs, Pie Charts, and Darwin]. He's famous because he knew Erasmus Darwin. He's also famous because there are stories that he took part in the Storming of the Bastille while living in Paris.

One the other hand, there are plenty of things for which he is less than famous [William Playfair] and there's a a good reason why his children left England and migrated to Canada becoming farmers near Perth, Ontario.


People I Met in Chicago at SMBE2013

I had a great time at SMBE2013 (Society for Molecular Biology and Evolution) in Chicago. Here are some of the people I met. I apologize for not including everyone—I forgot to take pictures of everyone I talked to.

I went to hear Masatoshi Nei give a talk on Monday morning (July 8) during a special session on "Ideas and Thoughts." The title of his talk was "Darwinism and the Theory of Mutation-Driven Evolution." This was the first time I had seen Nei in person and it was quite a thrill. I've been a huge fan ever since I read Molecular Evolutionary Genetics in 1987. That's when I first became aware of the power of population genetics and the importance of mutation and mutationism.

What Did Dan Graur Say in Chicago?

Dan Graur gave a fantastic and entertaining talk at SMBE2013 [Powerpoint]. He covered a lot of bases, but unfortunately left some out 'cause he had many slides that he didn't get to because of time limitations. Most of the audience enjoyed the talk very much—there was much laughter and enthusiastic head nodding. (I figure that two thirds of the audience agreed with his stance on junk DNA and ENCODE.)

Apparently Cornelius Hunter was in the audience because he blogged about it on Darwin's God: Dan Graur Gave a Great Talk This Week (copied on Uncommon Descent: Dan Graur Gave a Great Talk This Week). It's a shame he didn't make himself known to me or Reed Cartwright or Nick Matzke.

One of the things that Graur said was that if ENCODE is right then evolution is wrong. Now this may be a bit of an exaggeration, but not by much. If the ENCODE leaders are right that 85% of our genome has a biological function then we really do have to rethink the C-value paradox and genetic load. We also have to re-think a lot of biochemistry. I think that's what Dan meant. Cornelius Hunter says that's the one "glaring error" in Graur's presentation.

Theme

Genomes
& Junk DNA
Graur said that junk DNA is a "known known" and by that he means that there's plenty of evidence for junk DNA. It's not "dark matter" and we don't use the term "junk" to mask our ignorance. Speaking of ignorance, Cornelius Hunter seems to be completely unaware of any evidence for junk DNA. I guess he didn't stay to hear my presentation.


How Not to Do Science

Theme
Genomes
& Junk DNA
Many reputable scientists are convinced that most of our genome is junk. However, there are still a few holdouts and one of the most prominent is John Mattick. He believes that most of our genome is made up of thousand of genes for regulatory noncoding RNA. These RNAs (about 100 of them for every single protein-coding gene) are mostly involved in subtle controls of the levels of protein in human cells. (I'm not making this up. See: John Mattick on the Importance of Non-coding RNA )

It was a reasonable hypothesis at one point in time.

How do you evaluate a hypothesis in science? Well, one of the things you should always try to do is falsify your hypothesis. Let's see how that works ...
  1. The RNAs should be conserved. FALSE
  2. The RNAs should be abundant (>1 copy per cell). FALSE
  3. There should be dozens of well-studied specific examples. FALSE
  4. The hypothesis should account for variations in genome size. FALSE
  5. The hypothesis should be consistent with other data, such as that on genetic load. FALSE
  6. The hypothesis should be consistent with what we already know about the regulation of gene expression. FALSE
  7. You should be able to refute existing hypotheses, such as transcription errors. FALSE
Normally, you would abandon a hypothesis that had such a bad track record but true believers aren't about to do that. So what's next? Maybe these regulatory RNAs don't show sequence conservation but maybe their secondary structures are conserved. In other words, these RNAs originated as functional RNAs with a secondary structure but over the course of time all traces of sequence conservation have been lost and only the "conserved" secondary structure remains.1 The Mattick lab looked at the "conservation" of secondary structure as an indicator of function using the latest algorithms (Smith et al., 2013). Here's how they describe their attempts to prove their hypothesis in light of conflicting data ...
The majority of the human genome is dynamically transcribed into RNA, most of which does not code for proteins (1–4). The once common presumption that most non–protein-coding sequences are nonfunctional for the organism is being adjusted to the increasing evidence that noncoding RNAs (ncRNAs) represent a previously unappreciated layer of gene expression essential for the epigenetic regulation of differentiation and development (5–8). Yet despite an exponential accumulation of transcriptomic data and the recent dissemination of genome-wide data from the ENCODE consortium (9), limited functional data have fuelled discourse on the amount of functionally pertinent genomic sequence in higher eukaryotes (1, 10–12). What is incontrovertible, however, is that evolutionary conservation of structural components over an adequate evolutionary distance is a direct property of purifying (negative) selection and, consequently, a sufficient indicator of biological function The majority of studies investigating the prevalence of purifying selection in mammalian genomes are predicated on measuring nucleotide substitution rates, which are then rated against a statistical threshold trained from a set of genomic loci arguably qualified as neutrally evolving (13, 14). Conversely, lack of conservation does not impute lack of function, as variation underlies natural selection. Given that the molecular function of ncRNA may at least be partially conveyed through secondary or tertiary structures, mining evolutionary data for evidence of such features promises to increase the resolution of functional genomic annotations.
Here's what they found ..
When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional.
Apparently 13.6% of the human genome is a "large proportion." Taken at face value, however, the Mattick lab has now shown that the vast majority of transcribed sequences don't show any of the characteristics of functional RNA, including conservation of secondary structure. Of course, that's not the conclusion they emphasize in their paper.

Why not?

1. I can't imagine how this would happen, can you? You'd almost have to have selection AGAINST sequence conservation.

Smith, M.A., Gese, T., Stadler, P.F. and Mattick, J.S. (2013) Widespread purifying selection on RNA structure in mammals. Nucleic Acid Research advance access July 11, 2013 [doi: 10.1093/nar/gkt596]