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Wednesday, August 07, 2013

Carnival of Evolution #62: The Whig History

The latest issue of Carnival of Evolution is hosted by Joachim D, an evolutionary ecologist who blogs at Ecology and Evolution Footnotes. Read: Carnival of Evolution 62: The Whig History .
When it comes to the history of evolutionary theory, a whiggish image could look something like [the figure below]

I leave it to the readers to come up with a female version (including, for example, Maria Sibylla Merian, Rosalind Franklin, Barbara McClintock, Christiane Nüsslein-Volhard).

Arranging July's posts that I found interesting or entertaining as well as the few submitted by others according to a Whig history of evolutionary theory in the following is purely ornamental and does, of course, not imply any whiggishness on the side of the contributors.


If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Tuesday, August 06, 2013

Carnival of Evolution #61: Crustie Lovin; Edition

I was out of town when the last two Carnivals of Evolution were published so I'm doing a bit of catchup. The July issue of Carnival of Evolution was hosted by Marc Srour at Teaching Biology. He's the only blogger I know who is based in Cyprus. (He may have just moved to Japan.) Read: Carnival of Evolution #61: Crustie Lovin; Edition.
Hello, and welcome to the Carnival of Evolution #61. For this edition, I’ve chosen to celebrate what I perceive as an inexplicably underappreciated group of animals: the Crustacea. Of the major arthropod groups, I notice that crustaceans often get the short end of the stick. Everyone can name insects and recognise spiders, but besides seafood, crustaceans seem to be a question mark with most people. Insects and spiders have movies and songs written about them; crabs are the logo for cancer, the vernacular name for an STD, and they are an astrological sign.

Insulting. Crustaceans are awesome. There may be over a million insect species, but crustaceans take the cake when it comes to disparity, or morphological diversity, a measure in which no other taxon can match them.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Monday, August 05, 2013

Carnival of Evolution #60: Party like it’s 1953

I was out of town when the last two Carnivals of Evolution were published so I'm doing a bit of catchup. The June issue of Carnival of Evolution was hosted by Zen Faulkes at NeuroDojo. He's a invertebrate neuroethologist, whatever that is. Read: Carnival of Evolution #60: Party like it’s 1953.
Ladies and gentlemen, this is a special edition of the Carnival of Evolution. It’s the big six oh!

In honor of that achievement, we shall share this carnival’s space with other events celebrating their sixtieth anniversary.


If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Monday's Molecule #212

Last week's molecule was a thymine dimer. The winners were Alex Ling and Matt McFarlane. [Monday's Molecule #211].

Today's molecule is an important part of a major pathway. Give the common name and identify the pathway. Explain briefly why this pathway is important.

Email your answers to me at: Monday's Molecule #212. 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, August 04, 2013

Dear Denyse, Stop Digging

You're not going to believe what Denyse O'Leary just posted on Uncommon Descent: Junk DNA: Just because information is never used, doesn’t mean it is junk.
Further to Cornelius Hunter’s “Evolutionist: We do not promote any ‘spiritual ideologies,’” (in which he recounts that recent findings about RNA structure conservation suggest that even more of the mammalian genome is functional than supposed, hence there is less “junk DNA”:

I’ve never clearly understood Darwin’s fans attachment to junk DNA. It makes a good “anti-God” statement, as long as you are certain that the stuff is not and never could be any use. But that is precisely what is now widely contested. And it was a trap they need not have fallen into.

But a simple illustration will show that even if most of the information in DNA were never used, it would still be valuable. Let us say I have a directory of members of a club I belong to. I never use most of the phone numbers. Many numbers may never be used by anyone.

Does lack of use make that proportion of the directory junk?


Friday, August 02, 2013

Goodbye Dumpster

Jerry Coyne posted this video and I thought it was so funny I just had to put it on my website blog.



What Would Jerry Coyne, Daniel Dennett, and Richard Dawkins Do at Ball State University?

I'm trying to understand how the rules announced by President Jo Ann Gora would work in practice.

Let's think about how they might affect three prominent atheists. Jerry Coyne is an evolutionary biology professor at the University of Chicago. He is a prominent atheist and he defends the position that science and religion are not compatible. He does not have to adhere to the Ball State University rules because the University of Chicago is a private school.

Daniel Dennett is a philosopher at Tufts University (private). He is a prominent atheist and no friend of religion.

Richard Dawkins was a professor and evolutionary biologist at Oxford University in the UK. He did not have to worry about following the Ball State University rules because they don't apply outside of the USA.

Let's imagine that all three became professors at Ball State University. They would have to pay attention to the rules outlined by President Jo Ann Gora. Here are the relevant passages from her recent message.
Creation science, intelligent design, and other worldviews that focus on speculation regarding the origins of life represent another important and relevant form of human inquiry that is appropriately studied in literature and social science courses. Such study, however, must include a diversity of worldviews representing a variety of religious and philosophical perspectives and must avoid privileging one view as more legitimate than others.

As a public university, we have a constitutional obligation to maintain a clear separation between church and state. It is imperative that even when religious ideas are appropriately taught in humanities and social science courses, they must be discussed in comparison to each other, with no endorsement of one perspective over another.
All three professors have written extensively about religion and their views are widely known. They attend conferences and give public lectures. They do not pull any punches when they talk about the evils of religion. Nobody would ever say that they go out of their way to avoid endorsing one perspective over another. Academics have opinions and they are not afraid to express them.

Most professors have graduate students. They do not hide their opinions from their graduate students. Nor do they hide them from their colleagues or the administrators in their university.

These professors aren't shy about expressing their points of view on blogs, twitter, Facebook, newspapers and just any other means of communication.

Now let's imagine that they are teaching an undergraduate course about atheism and religion in a humanities department at Ball State University. How is that supposed to work? Are they supposed to go out of their way to avoid "privileging one view as more legitimate than others"? And if so, are any of the students going to be fooled? They can all access the internet.

It's clearly a ridiculous rule unless it also applies outside of the classroom. Does it mean that professors at a public university must avoid criticizing religion at all times?


President of Ball State University Forbids Teaching Intelligent Design

A few months ago Jerry Coyne learned that an astronomy professor (Eric Hedin) at Ball State University (Indiana, USA) was advocating an intelligent design perspective in his course on "The Boundaries of Science." Jerry contacted the Chair of the department to request that the administration intervene to prevent this professor from expressing his personal opinion in class. Jerry also contacted the Freedom From Religion Foundation and the FFRF lawyers sent a letter to Ball State University threatening them with a lawsuit for exposing students to intelligent design creationism in science class. Jerry Coyne, FFRF, and a host of others, think this course is forbidden by the US Constitution.

Thursday, August 01, 2013

The Junk DNA Controversy: John Mattick Defends Design

The failure to recognize the implications of the non-coding DNA will go down I think as the biggest mistakes in the history of molecular biology.

John Mattick
abc Australia
John Mattick has just published a paper dealing with the controversy over the ENCODE results and junk DNA. As you might imagine, Mattick defends the idea that most of our genome is functional. He attempts to explain why most of the critics are wrong.

The title of the paper is "The extent of functionality in the human genome" (Mattick and Dinger, 2013). It's published in the HUGO Journal. Recall that HUGO (Human Genome Organization) gave Mattick a prestigious award for his contributions to genome research. (See The Dark Matter Rises for a discussion of these contributions.)

UPDATE: Mike White also discusses this paper at: Having your cake and eating it: more arguments over human genome function.

Mattick's paper begins by mentioning three of the papers that were critical of ENCODE results: Dan Graur's paper (Graur et al. 2013), Ford Doolittle's paper (Doolittle, 2013), and the paper by Niu and Jiang (2013).

He begins by addressing one of Dan Graur's points about conservation.

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