Tuesday, January 31, 2012

Monday's Molecule #157

 
You need to pay close attention in order to identify this molecule correctly.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is L-sedoheptulose 1,7-bisphosphate or L-altro-hept-2-ulose 1,7-bisphosphate. The D isomer is part of the pentose phosphate cycle and the Calvin cycle. The winner is Peter Monaghan.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller

A Mormon Tale: Ontario to Nauvoo

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale

Ontario to Nauvoo


When we ended the first installment there were two families from Scotland living in Tosorontio township and Nottawasaga Township in southern Ontario. The Hood family and the Hill family came over from Scotland and settled originally in Dalhousie, in eastern Ontario. They moved south in the 1830s.

On April 6, 1832, Alexander Hill (born in 1811 in Scotland) married Agnes Hood (born in 1811 in Scotland). On Feb. 21, 1840, Isabella Hood (born in 1821 in Ontario) married Archibald Newell Hill (born in Scotland). They were married in Tosorontio where the Hill family farms were lcoated. Two brothers married Hood sisters. We are interested in the children of Isabella and Archibald. Recall that Isabella is the sister of William Hood and my wife and children descend from William.

UPDATE: The person in the photo is NOT the Isabella Hood Hill who is the mother of Hannah and the ancestor of Mitt Romney. Instead, it's the daughter of Isabella's sister who married Alexander Hill (see comments).

Archibald Newell Hill and Isobel Hood had two children while living in Canada. Samuel Hood Hill was born in Tosorontio on Dec. 23, 1840. Hannah Hood Hill was born in Tosorontio on July 9, 1842. She died in Colonia Juarez, Mexico in 1929 but a lot of interesting things happened in her life between those dates.

Monday, January 30, 2012

Religion is not on her radar ... and neither is something else

 
Heather Mallick published a column in today's Toronto Star where she declares that she is an atheist [Atheists should make more noise]. Good for her. We need more people to come out of the closet.

Why is she an atheist? It's not because she's opposed to religion it's because religion just isn't "on her radar." She just doesn't care about religion. In this sense she's not much different than most atheists: it's not that they actively study and reject any particular religion, they just don't believe in any gods.

I find it a bit strange that she and her husband ignore religion entirely. That seems like a recipe for disaster since religion is behind a lot of strife in today's world. But that's not what caught my eye when she described the topics that she and her husband do cover. There's seems to be a huge gap ... can you spot it? What else is sitting on the kitchen table?
If you like to stay current, you can’t simultaneously juggle all the elements that make up the news of the world. I follow politics, the arts, memoir and European history, with a minor in Spanish novelists, British comedy and American popular culture. My husband does economics, the history of the English language, meat-based cuisine, the novels of Graham Greene and soccer. The children have assigned themselves music, American fiction, social media and legal issues.

Religion sits on the kitchen table, orphaned.
I still love reading her columns in spite of her obvious deficiency!


A Mormon Tale: Glasgow to Ontario

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale
Glasgow to Ontario
James Hood was born on April 6, 1776 in Kelso, a small town south of Edinburgh near the border with England. His parent were William Robert Hood (1744-1799)1 and Hannah Clarke (1752-1832). James had six sisters (Agnes, Isabella, Margaret, Elizabeth, Hannah, and Mary) and one brother Dr. William Hood.

About five years after James was born, the family moved to Bridgeton in Barony Parish . At the time, Bridgeton was a small village, just north of the city of Glasgow. William Hood was employed there as a weaver and it’s quite likely that James also became a weaver at one of the factories in Barony.5

James Hood married Elizabeth Jones (1776-1803) in Barony on May 28, 1798. James and Elizabeth were both 22 years old. They had five children: William (1799-1894) (the direct ancestor of my wife and children), Jane (1800-1862), Elizabeth (1801-1875), Hannah (1802-1830), and Jean (1803-1803). Baby Jean dies shortly after birth and her mother, Elizabeth Jones, did not survive birth complications.

Sunday, January 29, 2012

Evolution of Horseshoe Crabs

 
The IDiots are at it again but this time they are aided and abetted by scientists who should know better. The subject is horseshoe crabs, famous as "living fossils" because species that look similar to the four living species were around millions of years ago.

The BBC (United Kingdom) is broadcasting a new television series called "Survivors"1 staring this month. The first episode is Horseshoe crabs are one of nature’s great survivors. The show is based on a book by Richard Fortey of the Natural History Museum in London, England.

Here's a quotation from the BBC press release where Fortey attempts to explain why horseshoe crabs haven't evolved.
A strange evolution?

Evolution not only brings about ‘improvements’ in body shapes and design that help a species adapt better to its surroundings. It also allows some species to remain basically the same.

‘These creatures tell us that evolution does not move inevitably forwards towards new morphology and new designs,' comments Fortey.

'Evidence for evolution is also found in past designs that endure to the present day. As long as the right habitat endures, then so will some of the creatures that inhabited the distant past.

Friday, January 27, 2012

The Problem With Press Releases

 
Press releases are a problem. Ryan Gregory has found a doozy: Radical Theory Explains the Origin, Evolution, and Nature of Life, Challenges Conventional Wisdom.

You may be tempted to actually read the paper. Don't. First, read what PZ Myers has to say: The comparison to jabberwocky is inevitable.


Paul Doty (1920 - 2011) and DNA Renaturation

Paul Doty was born in 1920. He died last month (Dec. 5, 2011) at his home in Cambridge, Massachusetts, USA [Paul Mead Doty (1920-2011)]. He was a Professor at Harvard for most of his career.

For many of us, Doty's major contribution to molecular biology was his study of DNA renaturation with his long-time post-doc and collaborator, Julius Marmur (1926 - 1996)1, a graduate of McGill University in Montréal, Canada. The paper that most of us remember is Marmur and Doty 1962: "Thermal Renaturation of Deoxyribonucleic Acids." This was the first time that the renaturation of complex DNA had been studied in detail and the results have led to many of the common techniques in use today.

Wednesday, January 25, 2012

Where Is David Attenborough?

 
Jerry Coyne has a little quiz for you as you watch this music video about evolution [An Evolution Music Video]. You should visit his blog website and answer the questions. Sandwalk readers should be able to answer the most difficult question namely, "Figure out where Attenborough is walking at the beginning: it’s a very famous place."




Monday, January 23, 2012

What's the Difference Between a Human and Chimpanzee?

The number of differences between the human and chimpanzee genomes is consistent with Neutral Theory and fixation by random genetic drift.

How Many Differences?

You can estimate the total number of single nucleotide differences by measuring the rate of hybridization of human and chimpanzee DNA in a technique developed by Dave Kohne and Roy Britten over forty years ago. This technique was applied to human and chimp DNA and the results indicated that the two genomes differed by about 1.5% (reviewed in Britton, 2002). That corresponds to 45 million bp in a genome of 3 billion bp.

This value of 1.5%, rounded up to 2%, gave rise to the widely quoted statement that humans and chimps are 98% identical. Britton (2002) challenged that number by pointing out that humans and chimp genomes differed by a large number of insertions and deletions (indels) that could not have been detected in hybridization studies. He claimed that there was an addition 3.4% of the genome that differed due to indels. That means the the real difference between humans and chimps is closer to 5% and we are only 95% identical!

Much of the difference is due to insertion and deletion of members of gene families. One study shows that the human genome has 689 genes not present in the chimp genome and chimps have 729 genes not present in humans [Mammalian Gene Families: Humans and Chimps Differ by 6%]. That's a total of 1,418 complete genes that are only found in one of the species.

At first glance this looks like 689 completely new genes have evolved in the human lineage since it diverged from our common ancestor with chimpanzees but looks can be deceiving. These genes are members of gene families and all that's happened is that 689 orthologous genes have either arisen by duplication in the human lineage or been lost by deletion in the chimp lineage or 689 new parologous genes have been "born" by gene duplication (or some combination).

Much better date is available today than in 2002 when Britten wrote his paper. We now know by direct comparison that there are at least 30 million single nucleotide differences between human and chimp genomes. There are about 90 million base pair differences as insertion and deletions (Margues-Bonet et al., 2009). The indels (insertions and deletions) may only represent 90,000 mutational events if the average length of an insertion/deletion is 1kb (1000 bp). In fact, more than 75% of indels are less than 5 bp (Britton 2002) so the actual number of mutational events is in the millions. Many of these are undoubtedly due to sequence errors. The latest studies indicate that humans and chimps differ by only 26,500 large indels (>80 bp) (Polavarapu et al., 2011). To a first approximation, the single nucleotide differences are a good measure of the total number of mutational events that have occurred in the two lineages. (underlined portion added on Jan. 25, 2012 - LAM)

Polymorphisms

It's worth noting that many of the differences between the human and chimp genomes are polymorphic within their respective populations. In other words, the variant alleles have not become fixed in the population. This affects the calculations of mutation rate since that calculation assumes that an allele has become fixed in the population by random genetic drift.

The polymorphisms include SNPs, of course, and that's the basis of many studies that look for specific haplotypes associated with disease. At least one of the variants at a given polymorphic locus in humans will be different from the nucleotide in the chimp reference genome. Deletions in the human and chimp genomes can also be polymorphic. Copy number variants (CNVs) in humans have been characterized in a number of studies (Campbell et al. 2011). In terms of total nucleotides, there is more variation in copy number than in single nucleotide polymorphisms (Alkan et al., 2011).

Are the Differences Neutral?

We would like to know if the differences between the human and chimp genomes are neutral alleles or if natural selection has played an important role in fixing these differences. Nobody doubts that many of the changes we see are adaptive in one or other of the lineages but can we recognize those important adaptive changes in a sea of possible neutral changes?

Several lines of evidence suggest that most of the changes are non-adaptive. First, since most (~90%) of the genome is junk, and most of the differences are located in junk DNA, it follows that most of the new alleles had no effect on function.

Second, if we look at the pattern of changes this is what we see for one of the human chromosomes.


The percent identity between humans and chimps fluctuates between 98% and 99% identity and the differences are pretty evenly scattered throughout chromosome 7. Remember, most of that DNA is junk.

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.

Motoo Kimura (1968)
The third line of evidence has to do with the mutation rate and fixation in the two lineages. The mutation rate in humans is about 130 mutations per generation based on our knowledge of the biochemistry of DNA replication [Mutation Rates]. A value that's consistent with recent direct measurements [Human Y Chromosome Mutation Rates] [Direct Measurement of Human Mutation Rate]. Michael Lynch (2010) bases his estimate of human mutation rates on a number of other studies. He comes up with a value of about 80 new mutations per generation.

In an evolving population the rate of fixation of neutral alleles is equal to the mutation rate [Random Genetic Drift and Population Size]. How many mutations would we expect in the human lineage since it diverged from a common ancestor with chimpanzees if all of the fixed alleles were neutral? The two species diverged about 5 million years ago. The average generation time in the human lineage is about ten years, so that means 500,000 generations. If the rate of mutation is about 100 new mutations per generation, then we would expect to see about 50 million new mutations in the human lineage. The actual number is about 22.5 million (half of 45 million). We're certainly in the right ballpark.

The actual mutation rate may be lower than we calculate.

We're certainly safe in concluding that the number of differences between humans and chimps is consistent with Neutral Theory and we should accept this as the null hypothesis.


Alkan C, Coe BP, Eichler EE. (2011) Genome structural variation discovery and genotyping. Nat Rev Genet. 12:363-376. [PubMed]

Britton, R.J. (2002) Divergence between samples of chimpanzee and human DNA sequences if 5%, counting indels. Proc. Natl. Acad. Sci. (USA) 99:13633-13636.

Campbell, C.D., Sampas, N., Tsalenko, A., Sudmant, P.H., Kidd, J.M., Malig, M., Vu, T.H., Vives, L., Tsang, P., Bruhn, L., and Eichler, E.E. (2011) Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet. 88:317-32. [PubMed]

Marques-Bonet, T., Ryder, O.A., and Eichler, E.E. (2009) Sequencing primate genomes: what have we learned? Annu. Rev. Genomics Hum. Genet. 10:355-386. [PubMed]

Lynch, M. (2010) Rate, molecular spectrum, and consequences of human mutation. Proc. Natl. Acad. Sci. (USA) 107:961-968. [PubMed]

Polavarapu, N., Arora, G., Mittal, V.K., McDonald, J.F. (2011) Characterization and potential functional significance of human-chimpanzee large INDEL variation. Mob. DNA 2:13. [PubMed] [doi:10.1186/1759-8753-2-13]

Monday's Molecule #156

 
This is one of the most important molecules on Earth. Without it we wouldn't be around and neither would most species. The revised structure is shown here. The one shown in the textbooks is wrong and this includes my own recently published edition of Principles of Biochemistry. Oops!

You need to identify the molecule, including the part with the white carbon atoms. You also need to specify how this molecule differs from the one shown in most textbooks.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is the iron-sulfur-molydenum cluster with bound homocitrate. The central atom was thought to be nitrogen but recent work has shown that it is most likely carbon. The cluster is in the active site of bacterial nitrogenase, an enzyme responsible for fixing atmospheric nitrogen and converting it to ammonia. This is a key part of the nitrogen cycle. The winner is David J. Schuller. I don't know if he will come for lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin

Sunday, January 22, 2012

The Modern Molecular Clock

The first molecular phylogenetic trees were constructed from the amino acid sequences of small proteins. One of those proteins was cytochrome c and it turned out to be very useful because homologues could be found in all species, including bacteria.

The original trees were published by Emanual Margoliash but I'm showing a later version here from Fitch and Margoliash (1967). This is a very famous tree that's found in many textbooks. (The version shown here is from Mulligan (2008).)

From the very beginning, the authors of these molecular phylogenetic trees noted that the rate of change in each lineage was approximately constant. You can see that in the tree shown here. The number of changes in the lineage leading to yeast (Saccharomyces) is 17+10+2=31 from the common root. The number of changes in the lineage leading to insects is 31 or 28, depending on the species. The number leading to humans and monkeys is 32.

Margoliash on "Homology" (1969)

Emanuel Margoliash (1920 - 2008) is famous for his studies of the evolution of cytochrome c genes/proteins. His lab sequenced dozens of them and he published some of the first molecular phylogenetic tress back in the early 1960s.

I recently stumbled on a letter he published in Science back in 1969 (Margoliash, 1969). It's about how you define "homology." This is one of my pet peeves. I've been trying to teach people for years that homology refers to the fact that two genes share a common ancestor. It a conclusion based on evidence such as sequence similarity. For example, if two genes/proteins are more than 30% identical over their entire length then you can conclude that they are homologous—they descend from a common ancestor. The conclusion is based on evidence, such as 30% sequence identity. Don't confuse "similarity" and "homology" because they are two different things.1

Homology is like being pregnant. Either you are or you aren't. You can't be 30% pregnant and you can't be 30% homologous.

I knew that the definition of homology had changed over the years but I didn't know that the dispute over its usage in molecular phylogeny started in the 1960s. Here's the Margoliash letter.
I regret the error in citation (the journal name was given as Nature, rather than Science), which crept in among the 462 references of the review (1) to which Winter, Walsh, and Neurath take exception (Letters, 27 Dec.). In that review, the term homologous was taken to imply, in parallel to universal biological usage, "that the genes coding for the polypeptide chains considered, in all the species carrying these proteins, had at one time a common ancestral gene," and we stated that when this concept is not intended "it would be best to use any of the numerous synonyms of 'similar' and 'similarity' and not appear to be prejudging the issue of evolutionary relations." The "pointed and specific criticism" followed, and was entirely contained in the sentence: "Other definitions may cause confusion and are unlikely to supplant well established biological usages." The "other definitions" referred to the article by Neurath, Walsh, and Winter (2), in which they state, "The term homology as applied to proteins refers to similarity in amino acid sequence," and later, that comparisons of protein structures "must be interpreted on a statistical basis lest we misinterpret random similarities."

On this last score there is no argument. Winter, Walsh, and Neurath will surely agree that in this field erroneous conclusions are likely to arise from the lack of an appropriate statistical distinction between random similarities and similarities of structure greater than can result from random phenomena. An excellent method of performing just such a distinction was published by Fitch (3), and although Neurath, Walsh, and Winter acknowledge it in their article (2), they do not use any acceptable statistical techniques in their comparisons of proteases. Thus, even by their own definition they fail to show "homology."

Homology, in any biological evolutionary context has a generally understood and well-defined meaning, namely the one we have adopted for use in protein primary structure comparisons. One cannot argue that such comparisons represent an area of knowledge separate from evolutionary biology, and that therefore one may use the same words for other meanings, since such protein studies obtain their interest largely in terms of evolutionary concepts and have their major impact in the taxonomic-evolutionary field. Winter, Walsh, and Neurath justify their novel definition of "homology" by maintaining that, without fossil remains, it is not possible to decide whether the structural genes corresponding to a set of present-day proteins are or are not ancestrally related. Apart from the inherent danger of assuming that a problem is insoluble, it may be pointed out that six pages after the definition of "homology," the paper (1) reviewed a statistical method for demonstrating just such ancestral homology. One requires enough primary structures to derive a "statistical phylogenetic tree," as has been possible in the case of cytochrome c (4). From such a tree a simple statistical calculation permits one to approximate the number of residues in a set of proteins that will remain invariant, because of biological necessity, no matter how many species are examined (5). If, in the comparison of any two proteins of this set, the number of identical residues is substantially in excess of the number that remain invariant in the entire set of proteins, then clearly this excess cannot result from functional convergence from different phylogenetic origins, a process yielding analogous structures, and, therefore, it can only be attributed to ancestral homology. In such a procedure, the assumption of the constancy of the genetic code has replaced the fossils of the morphological evolutionist.

Even if one does not accept the validity of such a demonstration, it is difficult to understand why there is an insistence on using the word "homology" for "similarities of protein primary structure greater than random." Any of the over 30 synonyms of "similarity" (6) or a variety of elegant neologisms would do, and prevent an insidious misunderstanding likely to arise in biological literature. Rather than take Alice in her confused trip in Wonderland as a model for logical scientific nomenclature, I prefer to follow the 17th-century poet reacting against a form of debasement of the language then prevalent, and "call a cat a cat" (7).

E. MARGOLIASH
Department of Molecular Biology,
Abbott Laboratories,
North Chicago, Illinois 60064
References

1. C. Nolan and E. Margoliash, Ann. Rev. Biochem. 37, 727 (1968).
2. H. Neurath, K. A. Walsh, W. P. Winter, Science 158, 1638 (1967).
3. W. M. Fitch, J. Mol. Biol. 16, 9 (1966).
4. W. M. Fitch and E. Margoliash, Science 155, 279 (1967).
5. W. M. Fitch and E. Margoliash, Biochem. Genet. 1, 65 (1967).
6. Roget's Thesaurus (St. Martin's Press, New York, 1965).
7. N. Boileau, Satires 1, line 52 (1660). "J'appelle un chat un chat, et Rolet un fripon."


1. Very few people pay attention to me. I appear to be fighting for a lost cause.

Margoliash, E. (1969) Homology: A Definition. Science 163:127

Friday, January 20, 2012

Understanding Mutation Rates and Evolution

The recent article by physician Joseph A. Kuhn contains a lot of errors and misunderstandings [Physicians Can Be IDiots]. Today I want to focus on one paragraph.
The complexity of creating two sequential or simultaneous mutations that would confer improved survival has been studied in the malaria parasite when exposed to chloroquine. The actual incidence of two base-pair mutations leading to two changed amino acids leading to resistance has been shown to be 1 in 1020 cases (42). To better understand this incidence, the likelihood that Homo sapiens would achieve any single mutation of the kind required for malaria to become resistant to chloroquine (a simple shift of two amino acids) would be 100 million times 10 million years (many times the age of the universe). This example has been used to further explain the difficulty in managing more than one mutation to achieve benefit.
The reference is to The Edge of Evolution by Michael Behe. His book was published in 2007 but I never got around to reviewing it thoroughly—partly because it's so difficult to explain where he goes wrong.1 Here's my take on one part of the book: The Two Binding Sites Rule. This post covers "chloroquine-complexity clusters" (CCC).

Thursday, January 19, 2012

Congratulations Vip!

 
Here's Vipulan Vigneswaran with his fabulous Biochemistry textbook that he won by contributing to Monday's Molecule [And the Winner Is ...]. Vip is studying Chemistry at the University of Toronto.


Alain de Botton Tells Us the Good Things About Religion

 
Here's a TED talk by Alain de Botton. He claims to be an atheist but he's promoting Atheism 2.0. That's a version of atheism that incorporates all the good parts of religion like how they can brainwash children and con people out of lots of money. And pilgrimage. Let's not forget the value of pilgrimage and the importance of travel. (Think Canterbury Tales!)

There's a certain mysticism about TED talks that I deplore. In order to be a successful TED talker you need to be articulate and clever. You need to be engaging and just a little bit radical—though not too radical. That's just about all it takes to get an enthusiastic standing ovation from the people who comes to listen to these 18 talks. What you're actually saying doesn't really count for anything as this example plainly shows.

The mantra of TED talks is "Ideas Worth Spreading" but if you think about it there aren't very many important new ideas that can be explained in 18 minutes. On the other hand, if you want to spread ideas that your audience already agrees with then TED talks are just the thing for you.




[Hat Tip: PZ Myers: Alain de Botton is right about one thing.]

James Shapiro Publishes on Evolution News & Views

James A. Shapiro, author of Evolution: a View from the 21st Century has been criticized for being an Intelligent Design Creationist, or at least a sympathizer. He denies it but his denials sound very much like someone who protests too much.

Shapiro has now been allowed to post an article on the main IDiot blog, Evolution News & Views [A Response to Ann Gauger's and Douglas Axe's Comments. I don't agree with his response but that's not the point. Do you know any respectable evolution supporter who would post on a creationist blog?

Can you imagine his University of Chicago Colleague, Jerry Coyne, posting an article on the flagship blog of the Discovery Institute?


Physicians Can Be IDiots

 
Joseph A. Kuhn is a physician at the Baylor University Medical Center at Dallas. This is a Christian medical center associated with Baylor University in Waco, Texas. Joseph Kuhn published an article in a recent issue of Baylor University Medical Center Proceedings: Dissectring Darwinism.

Kuhn has an M.D. degree. He is not a scientist and he has no obvious expertise in biology and/or evolution. He is a Roman Catholic. He is definitely an Intelligent Design Creationist.

Let's look as what this IDiot has to say ...
The primary conflicts or anomalies with neo-Darwinian evolution lie in the failure of mutation and natural selection to account for the formation of DNA, the information of DNA, or the complexity of the human cell. In all fairness, many physicians, medical students, and college students have not been shown the weakness of Darwinian evolution. They haven’t been shown the failure of the Miller-Urey experiments to explain DNA, RNA, or protein formation; the paucity of fossil data; or the refutations of transitional species based on a growing biochemical understanding of complex systems and the limits of DNA mutation to account for the formation of new DNA, new chromosomes, and therefore new species.

In contrast, how is it possible that the majority of National Academy of Science members (who should know the above weaknesses) fully believe that random mutation and natural selection can explain the origin of DNA and the subsequent generation of a vast array of protein systems within complex cells? It is possible that the biologist, the paleontologist, and the anthropologist are each studying a small portion of the picture and do not have the education and training to see the full picture. More likely, their previous research relies on the established paradigm of Darwinian evolution to provide structure for their work. As the limitations of existing paradigms become apparent, adoption of a new paradigm typically requires at least a full generation, since existing practitioners and scientists often hold on to the old paradigm.
There's so much wrong here that I hardly know where to begin. First, biological evolution, whether it be the outmoded neo-Darwinian model or a more modern version, was never intended to explain the origin of life. We don't know how life originated but that has nothing to do with the truth and power of evolution as an explanatory mechanism.

Second, members of the National Academy of Science—and all other scientists in the USA and many other countries—are not stupid. The idea that they would all fail to see the truth about evolution because they "do not have the education and training to see the full picture" is silly beyond belief. The idea that they might be blind to the truth because they adhere to an incorrect Darwinian paradigm is ridiculous. The idea that a physician at a Christian university might be in a better position to recognize the truth about evolution is something that only a true IDiot could believe.

The standard IDiot talking point these days is that students and the general public are being misled because scientists won't teach all the problems and controversies concerning biological evolution. This is an attitude that completely ignores all the debate and discussion that has been taking place on the internet and in popular books, magazines, and journals over the past four decades. None of the problems and controversies have stood up to close analysis in spite of the fact they have been dogmatically defended by dozens of leading IDiots.

Of course Joseph Kuhn, the physician, knows nothing about this. That's why he writes ...
When the Texas State Board of Education voted to recognize the weaknesses of Darwinian evolution in explaining the origin of the species, it was a result of 3 full days of intense debate and scientific dispute. In 2011, when new textbooks were presented to the State Board of Education, 9 out of 10 failed to provide the mandated supplementary curricula, which would include both positive and negative aspects of evolution (44). Moreover, several of the textbooks continued to incorrectly promote the debunked Miller-Urey origin of life experiment, the long-discredited claims about nonfunctional appendix and tonsils, and the fraudulent embryo drawings from Ernst Haeckel. In essence, current biology students, aspiring medical students, and future scientists are not being taught the whole story. Rather, evidence suggests that they continue to receive incorrect and incomplete material that exaggerates the effect of random mutation and natural selection to account for DNA, the cell, or the transition from species to species.

The Texas State Board of Education guidelines do not propose teaching any other alternatives to Darwinian evolution. Rather, the students of tomorrow and teachers of today should appropriately recognize that there are weaknesses that have been pointed out by reasonable scientists. In this dissection of Darwinism, we have cut into the weaknesses of the fossil evidence for human evolution, the failure of the fossil data to demonstrate substantial transition species, and the awareness of the sudden formation of most species in a short window of time, with no significant subsequent variation. More importantly, this physician-perspective article emphasizes the extreme impossibility of the natural formation or self-formation of billions of nucleotides in a specific sequence, allowing for the coding of RNA and proteins in a complex cell with thousands of interrelated and irreducibly complex functions. The article also enlightens the reader regarding the conflicts and difficulty of using natural selection and mutation to explain the simultaneous or sequential changes in cellular DNA, involving entirely new strands of DNA and thousands of new proteins, which are necessary for the formation of new species.
It's hard to imagine what must be going on inside the head of someone who could write such drivel. Let's say that the Texas Board of Education succeeds in brainwashing students about the "weaknesses" of evolution. Is that going to change the minds of any expert who studies biological evolution for a living? Is that going to lead to a new generation of scientists who accept Intelligent Design Creationism? No, not even in Texas.

Only an IDiot could believe that forcing Intelligent Design Creationism down the throats of students in some parts of southern USA will eventually lead to a "paradigm shift" in thinking about evolution. Only an IDiot physician could believe that he knows more about evolution than the experts. In fairness, you've got to give the creationists some credit for convincing some, otherwise intelligent, people that 99.9% of all scientists are really, really stupid.

UPDATE:Jonathan Wells defends Joseph A. Kuhn, MD ["Shut up," Coyne Explained].


[Hat Tip: Jerry Coyne in Creationist paper in a medical journal.]

Canadian Blog Awards: Science and Technology

 
Voting for The Canadian Blog Awards ends tomorrow so this is your last chance to pick the best of the best(?).

Most of you will be interested in the science blogs. The category is Best Science and Technology Blog. Here are the finalists ...

Sync.ca
Here at Sync, we strive to bring you the latest in news, reviews and opinions from the tech universe. It′s our way of helping to keep Canadians in sync with tech and gadgets that surround us in our daily lives. Never miss a beat: stay in Sync.
iPhoneinCanada.ca
iPhoneinCanada.ca was started in late 2007 in Vancouver, BC. The site was created to document using the first generation iPhone in Canada. The blog has evolved along with the iPhone and we are now the leading Canadian iPhone authority for news, reviews, tips, tricks and anything else iPhone-related. We are powered by a fantastic iPhone community.
Jon Arnold's Analyst 2.0 Blog
Independent analysis of the IP communications sector - VoIP, Mobile Broadband, IPTV, Unified Communications, Telepresence, Mashups, Web 2.0, Social Media, etc. Plus, my thoughts on all the other things I enjoy during the rest of the day like the Red Sox and great music. And more recently, Smart Grid too!
Hi-Sci-Fi
Creator, producer, writer and host of HiSciFi is Irma Arkus. Over the years, she noticed that the idea of sitting by herself in a studio is unappealing, and potentially dangerously unfunny too. So, Irma had quite a few lovely co-hosts over the years: Andrew Yang, Jevon Ryan, Gregory Milne, and Tarek Suliman. Irma is evidently a man-eater.

BROADCASTING OF HISCIFI

HiSciFi is taped and broadcast live, every Friday at 5:00-6:00 p.m. on CJSF 90.1FM in Burnaby, British Columbia, Canada. Currently, HiSciFi is evaluated for syndication.

www.HiSciFi.com is the place where the show gets a second life as a podcast, and as such can be found at numerous podcast distribution sites, as well as distributed by Mininova.org, PirateBay.com and BTJunkie.org via bit-torrent.
Mark Evens Tech
My company, ME Consulting, creates digital strategies and does tactical execution for startups and entrepreneurs that want to take their marketing efforts to the next level. Having worked for startups, covered them a reporter and consulted with them for the past three years, I understand their goals, and what they need to be successful.
Hmmm ....

There seems to be a slight problem. There are no "science" blogs in the running for best science and technology blog! This is one of my pet peeves. Why can't people understand the difference between science and technology?

When's the last time you saw an actual science project win a Science Fair?

If you really want to cast a vote then go to Best Religion and Philosophy Blog and vote for Canadian Athiest.


Wednesday, January 18, 2012

False Dichotomy

 
A false dichotomy is when you are presented with two choices and told that if one is wrong then the other must be correct but there are actually other choices.

Intelligent Design Creationists are very fond of this argument. They tell you that there are only two choices when it comes to explaining biology: either Darwinism or Intelligent Design Creationism. If a given feature of the biological world cannot possibly be explained by Darwinism, then God must exist and he must have designed the feature.

Here's Douglas Axe illustrating the false dichotomy on Evolution News & views [Let Science Be the Arbiter: A Reply to James Shapiro].
As an ID proponent, I've put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

There is no crutch here. The aspects of protein structure that appear to preclude a naturalistic origin have been described in detail. If Shapiro or anyone else were to show in detail how these are overcome by a naturalistic mechanism, then my argument would fall and I would let it fall. But the reverse needs to be true as well. Scientists who personally side with naturalism have to be willing to let naturalism fall, as otherwise they would be guilty of using a crutch to prop it up.
This is actually an attempt to get around the charge of false dichotomy by extrapolating from a rejection of Darwinian explanations to any naturalistic explanation. If Axe is truly able to demonstrate that his "data" cannot possibly be explained by any naturalistic means then it follows logically that the only other type of explanation has to be supernatural. But what Axe is really arguing against is a Darwinian explanation and it's only his lack of imagination and arrogance that allows him to claim that no other naturalistic explanation is possible.

As we have seen time after time, the Intelligent Design Creationists do not have a scientific theory or any kind of scientific explanation for biological phenomena. All they have is criticisms of science—criticisms that are usually based on a lack of knowledge. When will we see an ID explanation of protein folding and function?


The 2012 Edge Question

 
John Brockman is, among other things, a literary agent with a large stable of famous scientists. He runs a website called The Edge and every year he asks a question and solicits responses from his clients and admirers. This year's question is WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION?
Scientists' greatest pleasure comes from theories that derive the solution to some deep puzzle from a small set of simple principles in a surprising way. These explanations are called "beautiful" or "elegant". Historical examples are Kepler's explanation of complex planetary motions as simple ellipses, Bohr's explanation of the periodic table of the elements in terms of electron shells, and Watson and Crick's double helix. Einstein famously said that he did not need experimental confirmation of his general theory of relativity because it "was so beautiful it had to be true."

WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION?

Since this question is about explanation, answers may embrace scientific thinking in the broadest sense: as the most reliable way of gaining knowledge about anything, including other fields of inquiry such as philosophy, mathematics, economics, history, political theory, literary theory, or the human spirit. The only requirement is that some simple and non-obvious idea explain some diverse and complicated set of phenomena.

Here are some of my favorites ....

My Favorite Annoying Elegant Explanation: Quantum Theory by Raphael Bousso
Life Is a Digital Code by Matt Ridley
Plate Tectonics Elegantly Validates Continental Drift by Paul Saffo
Watson and Crick Explain How DNA Carries Genetic Information by Gary Klein
Atomism: Reconciling Change with No-Change by Marcelo Gleiser
The 19th Century Explanation of the Remarkable Connection Between Electricity And Magnetism by Lawrence M. Krauss
We Are Stardust by Kevin Kelly
The Principle of Empiricism, or See For Yourself by Michael Shermer

Here are some of my not-so-favorites ....

Fitness Landscapes by Stewart Brand
Sexual Conflict Theory by David M. Buss
Pascal's Wager Tim O'Reilly
Epigenetics by Helen Fisher
Evolutionarily Stable Strategies by S. Abbas Raza
The Destructive Wrath of the General Purpose Computer by Jordan Pollack
Subverting Biology by Patrick Bateson
Sex At Your Fingertips by Simon Baron-Cohen
The Epidemic of Obesity, Diabetes and "Metabolic Syndrome:" Cell Energy Adaptations in a Toxic World? by Beatrice Golomb
Why We Feel Pressed for Time by Elizabeth Dunn
Why Some Sea Turtles Migrate by Daniel C. Dennett
Evolutionary Genetics Explains The Conflicts of Human Social Life by Steven Pinker
The Faurie-Raymond Hypothesis by Jonathan Gottschall
The Gaia Hypothesis by Scott Sampson
The Elegant Robert Zajonc by Richard Nisbett



Scientists vs. Science Writers

 
Follow the discussion on Ed Yong's blog Not Exactly Rocket Science [Every scientists-versus-journalists debate ever, in one diagram].



The main problem isn't represented on the diagram. It's when good/bad journalists write articles in praise of bad science.

Monday, January 16, 2012

What Does a Secular Society Look Like?

 
Casey Luskin wonders What Would the World Look Like if the New Atheists Won the Day?. He's just read Penn Jillette's new book, God, No!: Signs You May Already Be an Atheist and Other Magical Tales, and he's "discovered" by selective quote mining that Penn would persecute Christians if the atheists ever gained power in America.

This leads Casey to speculate on what the secular world would look like if people abandoned their religion. He imagines that it won't be a nice place.
Back to the Secular Decade. If there's one thing to admire about Penn Jillette, it's that he's transparent about what he really thinks. If only more "new atheists" were so transparent, then the public might get a more realistic picture of what Faircloth's "Secular Decade" would really look like.
If Casey had been paying attention, he wouldn't have to look very far. Many European countries are well on their way to being truly secular societies. In the Netherlands, for example, only 34% of the population believes in God [Demographics of atheism]. If the New Atheists were to succeed in America then most people would abandon religion and life would go on pretty much as usual except that the society would become more rational, more understanding, and more tolerant. Creationism would become a joke, gays could marry, and women would have the right to choose. That's what's happened in the Netherlands and many other civilized countries.


Photo Credit: Amsterdam Tourism & Convention Board

The Mind of James Shapiro

I recently read Evolution: a View from the 21st Century by James Shapiro. It was a very annoying and frustrating experience. I do not recommend this book. I've already posted a rebuttal of his silly claim that the Central Dogma of Molecular Biology needs to be revised [Revisiting the Central Dogma in the 21st Century ]

The really frustrating part was trying to figure out Shapiro's agenda. He clearly has one. Is it just that he's against "conventional evolutionary theory"—whatever that is? Or, is he laying the groundwork for introducing God and intelligent design?

Shapiro denies that he's a supporter of intelligent design yet he published several papers with Richard Sternberg, one of the darlings of Intelligent Design Creationism. Furthermore, he (Shapiro) uses many of the same anti-evolution arguments used by Intelligent Design Creationists.

This prompted Bill Dembski to accuse James Shapiro of "dancing in the DMZ between Darwin and design" [Is James Shapiro a Design Theorist?].
For proponents of intelligent design, James Shapiro's constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.
This got a response from Shapiro that has now been posted on Evolution News & Views ["Is James Shapiro a Design Theorist?": James Shapiro Replies]. Here's what Shapiro says ...

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.
Clear as mud. There's one thing I know for sure: horizontal DNA transfer etc. are perfectly compatible with today's evolutionary thinking. If Shapiro is wrong about this—and he is— then maybe he's also misleading us about his belief in intelligent design creationism.

Saturday, January 14, 2012

Phytoplankton Blooms

 
This is a spectacular view of a phytoplanton bloom in the South Atlantic. It was taken by the Envisat satellite on Dec. 2, 2011 [A Southern Summer Bloom].

These phytoplankton blooms usually consist of a single species of microorganism. The fact that they can be seen from space gives you an idea of just how abundant they are. The blooms in the oceans can be due to diatoms or algae but by far the most common large blooms are due to cyanobacteria.

Prochlorococcus sp. and Synechococcus sp. have the largest population sizes of any species on the planet. About 30% of all oxygen production on the planet is due to marine phytoplankton and these two species account for a significant proportion.

A third genus of cyanobacteria, Trichodesmium, is mostly found off the coast of Australia. In addition to producing oxygen by photosynthesis, it is responsible for a considerable proportion of nitrogen fixation in the oceans.


[Hat Tip: Bad Astronomy]

Turn Off Your Irony Meters Before Reading This!!!

Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters. They were always being fried by outrageous comments from the anti-science creationists. New, more powerful, irony meters were needed every few months.

The following post appeared on Uncommon Descent today: Is this where science fraud begins?. You are about to read an excerpt but I caution you to turn off your irony meter unless it's a Mark IX (beta) version. Even then, I'm not sure it will survive.

Denyse O'Leary quotes from an article published on Defining Ideas: The Death of Honesty by William Damon.
In July 2011, a widely-reported cheating scandal erupted in school systems in and around Atlanta, Georgia. State investigators found a pattern of “organized and systemic misconduct” dating back for over ten years. One-hundred-and-seventy-eight teachers, and the principals of half of the system’s schools, aided and abetted students who were cheating on their tests. Top administrators ignored news reports of this cheating: a New York Times story described “a culture of fear and intimidation that prevented many teachers from speaking out.”

Nor was this an isolated incident. In a feature on school testing, CBS News reported the following: “New York education officials found 21 proven cases of teacher cheating. Teachers have read off answers during a test, sent students back to correct wrong answers, photocopied secure tests for use in class, inflated scores, and peeked at questions then drilled those topics in class before the test.”

With such prominent and recent instances of cheating among students and teachers today, one would expect a concerted effort to articulate and promote the value of honesty in our schools. Yet school programs regarding academic integrity consist of little more than a patchwork of vaguely-stated prohibitions and half-hearted responses. Our schools vacillate between routine neglect and a circle-the wagons reaction if the problem boils over into a public media scandal. There is little consistency, coherence, or transparency in many school policies.
Let's think about the 178 teachers in schools around Atlanta, Georgia. It's pretty safe to assume that the vast majority of those teachers are god-fearing Christians and most of them don't accept evolution.

So, how does Denyse O'Leary explain why unethical behavior among teachers is so rampant?
The most likely reason is that the educators involved do not believe that anyone has made a free choice to cheat or that cheating is an ethical issue.

Chalk another one up to the high cost of evolutionary psychology and related trends.


Friday, January 13, 2012

Life: You Know It When You See It

 
Carl Zimmer, who blogs at The Loom, is interested in definitions of life. His latest essay highlights a definition proposed by Edward Trifonov who says that life is: "self-reproduction with variations" [Can A Scientist Define “Life”?].

It didn't take Sean Carroll (the physicist) very long to see one of the main problems with this definition; namely that Sean isn't alive! [Do I Not Live!].

It's true that we should not restrict our definition of life to things that can self-reproduce. It's also true that we should not restrict our definition to things that reproduce badly (e.g. mutation/variation). I can easily imagine living things that could reproduce perfectly—they just wouldn't evolve by any mechanism we currently recognize.

Life is like pornography [I know it when I see it]. In the words of US Supreme Court Justice Potter Stewart,
I shall not today attempt further to define the kinds of material I understand to be embraced within that shorthand description ["hard-core pornography"]; and perhaps I could never succeed in intelligibly doing so. But I know it when I see it, and the motion picture involved in this case is not that.


Wednesday, January 11, 2012

Weep for the Poor Persecuted IDiots

 
The Intelligent Design Creationists at Evolution News & Views and Uncommon Descent have been pushing the idea that acceptance of evolution is associated with moral decay and the rise of Adolph Hitler. Recently, an IDiot going by the pseudonym of "kairosfocus" posted a similar attack on his blog: Visually exposing the Anti-Christ spirit of Nazism (and correcting the New Atheist "Hitler was a Christian" smear often used in retort to exposing* the Social Darwinist history of ideas roots of Hitler's thought.

The goal, obviously, is to link the scientific fact of evolution to the evils of social Darwinism and eugenics.

Somebody posted as comment on that blog (or a related blog) saying ...
xxx, the religious wacko who owns and runs this site, blames all the world’s ills, including Hitler and the nazis, on Darwin, atheists, and material evolutionists.

To see the truth about Hitler and the nazis, see these XXXXXXX:

XXXXXX is a LYING, arrogant, bloviating, sanctimonious, ignorant, uneducated, abusive, delusional god zombie.

See this site for a lot more about XXXXX:
The comment has been removed.

Now "kairosfocus" has complained on Uncommon Descent that such "vandalism" is outrageous and misguided [FOR RECORD: What we are dealing with . . . an example of web stalking and vandalism].
Now, this vandalism of a site wholly unrelated to the matters debated at UD (and tied onwards to a hate site that exploits Google’s freedom of comment policies), was evidently in response to my having posted here at UD, matters linked to the well-known history of ideas roots of Hitler’s thought. I therefore suggest that onlookers examine the Weikart lecture and a discussion of a key clip from Mein Kampf that demonstrated the Darwinist-Haeckelian frame of thought, that beyond reasonable doubt strongly shaped Hitler’s thinking, speech and behaviour. (Those needing documentation on Hitler’s actual attitude to and intentions for the Christian Churches, can look at the recently released Nuremberg investigatory documents here. If after seeing these documents and the like, someone still insists on trying to claim Hitler was a Christian etc etc, s/he is delusional and/or willfully deceitful.)
Furthermore, the behavior of this "vandal" is exactly what "kairosfocus" expects.
As they say, a tree is known by its fruits, and draws sustenance from its roots . . .

(In addition, a note on “blaming the world’s ills.” The likes of this hate-driven commenter will not appreciate or accept that a Bible-believing Christian will hold that much of what ails our world traces to our common challenge of being finite, fallible, morally fallen and too often ill-willed. Hence, our common need for recognition of our moral plight, repentance, forgiveness and moral-spiritual transformation through the gospel. Slander-laced strawmen and scapegoats are ever so much more easy to set up and ignite through irresponsible rhetoric that then clouds, polarises and poisons the atmosphere.)

That refusal to be responsible over a moral hazard closely tied to the Darwinist, evolutionary materialist frame of thought, and that refusal to acknowledge well-established historical facts that are inconvenient to the new atheist agenda are tellingly informative.

The pattern of obsessive, self-justifying, nihilistic hate, stalking, slander, Internet vandalism and abuse is even more informative about an unfortunately significant subset of the New Atheist movement and the danger its patent extremism poses. (After this sort of web vandalism, and worse, can any reasonable person doubt why moderation is necessary to maintain a reasonable tone at UD and elsewhere?)

Ironically, the very conscience benumbed self-justifying by smearing scapegoats that this sort of behaviour demonstrates on the small scale, is what — when such attitudes attained state power — led to the utter breakdown of morality on the grand scale that over 100 million ghosts from the past century tell us never to forget.

Can any reasonable person doubt that had a commentator like the above the power to do as he wished and get away with it, he would do me and my family further harm?

It is time for the New Atheist advocates of evolutionary materialism to take a serious look at what they have been enabling by their intemperate writings and attitudes.
Every atheist blogger gets far worse comments from Christians on a regular basis. Most of us get harassing emails every single day and the authors usually identify themselves as devout Christians doing God's work. These same Christians don't hesitate to send threatening messages to our colleagues and family members in an effort to silence us. Some of the Christian kooks are so dangerous that they have been arrested by police and are currently under forcible confinement in a mental health institution.

Don't weep for the IDiots. They need to examine their own beliefs since it's the creationists who are the biggest threat on these blogs. There must be something wrong with Christianity if that's the kind of activity it promotes. It is time for the Christian opponents of science to take a serious look at what they have been enabling by their intemperate writings and attitudes.


Monday, January 09, 2012

Monday's Molecule #155

 
We're going to talk about the evolution of this molecule in my class tomorrow. It's a good examples for illustrating some basic principles of molecular evolution.

You need to identify the exact molecule, including the species. Here's a hint: ANKSKGIVWN.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The winner is Dima Klenchin who was the first to identify the molecule as cytochrome c from tuna (Thunnus alalunga). The figure is from the PDB file 3CYT. This PDB file supercedes 1CYT which was reportedly from another species of tuna.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody


Saturday, January 07, 2012

Recent Advances in Intelligent Design Creationism

 
In case you missed it, 2011 was a wonderful year for the IDiots. There were many "scientific" breakthroughs supporting the existence of god an intelligent designer. Access research network provides a list of the top ten "Darwin and Design" news stories for 2011.

I'll just give you the titles. Most of you have already read these very important science papers. The rest of you can access more information at: Top Ten Darwin and Design
Science News Stories for 2011
.
  1. 50th Peer-Reviewed Pro-ID Scientific Paper Published
  2. The Design of the Butterfly Continues to Inspire and Amaze
  3. Woodpecker Drumming Inspires Shock-Absorbing System
  4. Stylus Aims to Bridge Gap Between Real World and Artificial Evolutionary Simulation
  5. Explosive Radiation of Flowering Plants Confirmed
  6. Golden Orb-Weaver Fossil Spider Provides New Evidence for Stasis
  7. Complexity in the Universe Appears Earlier Than Thought
  8. An Identity Crises for Human Ancestors
  9. DNA Repair Mechanisms Reveal a Contradiction in Evolutionary Theory
  10. The Limits to Self-Organization Identified
The nice thing about this list is that it gives us a very good view of the quality of data supporting Intelligent Design Creationism. This is the best they have.


The God helmet is used by Michael Persinger in his neuroscience "research." When you put on the helmet it makes you see God. It's just one of many illusions that supposedly reveal the presence of a supernatural being. Of course it has nothing to do with the content of this post.

The Santorum Amendment

 
Rick Santorum is a potential candidate for President of the United States. He is currently seeking the nomination of the Republican party and so far he seems to be a leading candidate in spite of his bizarre views on many issues. The process involves things called state "primaries" which seems to be a way of generating free publicity for the two sanctioned parties.

Back in 2001, Santorum was a Senator from Pennsylvania. He was a leading proponent of Intelligent Design Creationism and he proposed an amendment to a major education bill that was being considered by the United States Senate.1 The original Santorum Amendment was described by Santorum in a brief speech ...
This is an amendment that is a sense of the Senate. It is a sense of the Senate that deals with the subject of intellectual freedom with respect to the teaching of science in the classroom, in primary and secondary education. It is a sense of the Senate that does not try to dictate curriculum to anybody; quite the contrary, it says there should be freedom to discuss and air good scientific debate within the classroom. In fact, students will do better and will learn more if there is this intellectual freedom to discuss. I will read this sense of the Senate. It is simply two sentences—frankly, two rather innocuous sentences—that hopefully this Senate will embrace: "It is the sense of the Senate that—

(1) good science education should prepare students to distinguish the data or testable theories of science from philosophical or religious claims that are made in the name of science; and
(2) where biological evolution is taught, the curriculum should help students to understand why this subject generates so much continuing controversy, and should prepare the students to be informed participants in public discussions regarding the subject.

It simply says there are disagreements in scientific theories out there that are continually tested.
The original amendment was drafted by Philip Johnson in consultation with other fellows of the Discovery Institute.

This amendment did not make it into law but a similar version was included in something called a "Conference Report" where it is often cited by Intelligent Design Creationists.
The Conferees recognize that a quality science education should prepare students to distinguish the data and testable theories of science from religious or philosophical claims that are made in the name of science. Where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society.
Taken at face value, these statements seem to provide an excellent opportunity for science teachers to explain how religion distorts science. They would provide legal justification for teachers who want to describe how religious views conflict with science and why scientific facts, such as evolution, generate so much controversy among religious Americans.

But that's not how the amendments are interpreted by most people. Here's Rick Santorum explaining in 2009 what the amendment really meant. It's clear that many Senators, including Ted Kennedy, were duped.




1. In American legislatures, it's normal that completely irrelevant material is inserted into bills.

Should Undergraduates Study the Primary Scientific Literature?

 
The short answer to the question posed in the title is "yes" but there are many caveats. One of them is that it depends on what level you are teaching. In my opinion, the value of exposing science students to the primary scientific literature (papers) increases as students progress from first year to the year they graduate. Students in their final year of a science program will gain a lot from being exposed correctly to the scientific literature but students in introductory course will hardly benefit at all—and may, in fact, be harmed if it takes time away from learning basic principles and concepts.

It is important to teach critical thinking and it's important to focus education on basic principles and concepts. Most of the basic principles and concepts in a discipline have been developed over several decades. The work that led to those ideas is (usually) in the primary scientific literature but you can't learn the concept by just reading a few key papers. Evolution is a good example but so is our understanding of how cells generate energy from proton gradients, how enzymes work, and how the information in messenger RNA gets translated into proteins.

I find it helpful to remind myself from time to time that the vast majority of the students I teach will never be scientists and many of them aren't really interested in how to do scientific experiments. They will become average citizens in all kinds of careers that have nothing to do with the basic sciences. Our goal is to make them scientifically literate so they will understand why evolution is true, why homeopathy is bunkum, why they should vaccinate their children, and why humans are behind global climate change. I don't think we can achieve that goal by focusing on the primary scientific literature, especially in the early years of undergraduate education.

C.R.E.A.T.E. is a education project funded by the United States National Science Foundation (Grant No. 1021443). It's goal is "transform understanding of science" by using the primary scientific literature as a teaching tool. Here's how they describe their approach ...
The C.R.E.A.T.E. (Consider, Read, Elucidate the hypotheses, Analyze and interpret the data, and Think of the next Experiment) method is a new teaching approach that uses intensive analysis of primary literature to demystify and humanize research science for undergraduates. Our goal is to use the real language of science—the journal article—as an inroad to understanding “who does science, how, and why?” At the same time, we wish to help students (1) experience authentic processes of science, in particular discussion/debate about experimental data and their interpretation (including ‘grey areas’), (2) recognize the creativity and open-ended nature of research, and (3) see the diversity of people who undertake research careers (i.e. not just the genius/geeks of popular culture). As a complement to teaching based on textbooks, which tend to oversimplify the research process, C.R.E.A.T.E. teaching focuses on on authentic published work--peer reviewed journal articles—with students reading either series of papers produced sequentially from individual labs or series of papers from different labs focused on a single line of research.

By reading/analyzing a set of papers published in series from a single lab, students experience the evolution of research projects over a period of years. Using newly-developed C.R.E.A.T.E. pedagogical tools, that encourage multiple approaches to the material (concept mapping, sketching, visualization, transformation of data, creative experimental design) students gain deep understanding of the methods (and biological content/principles) that underlie each individual experiment of the paper. In class, we emphasize scientific thinking--focusing on understanding both why and how each part of the study was done, by examining the hypotheses underlying each aspect of the study, and analyzing/discussing the data represented in each figure and table. Students learn to interpret complex data, draw conclusions, debate interpretations, and re-represent data (e.g. represent tabled data in graphic form) to aid understanding. Content knowledge is reviewed as students consider the principles underlying the techniques used, as well as the overall context of the scientific question being addressed (e.g. a module focused on regeneration would likely include review multiple aspects of cell division, cell differentiation, gene expression and stem cells, drawing on information students learned in other classes and helping them to apply it in a real-world research situation). C.R.E.A.T.E. students thus learn a variety of transferable learning skills that can be applied to complex scientific reading they do in the future. Students design their own proposed followup experiments at several points in the semester, and debate each other’s proposed studies in a classroom exercise modeled on activities of bona fide scientific grant panels. Such discussions reveal the research process to be openended, with multiple branch points or possible “next directions to go;” thus much less linear and predictable than many students expect. Late in the process, students generate a short list of questions for paper authors that are sent as an email survey to each author (not simply the PI). Responses from multiple authors provide unique behind-the-scenes insight into “the people behind the papers,” humanizing the research experience and showing researchers to be complex individuals much like the students themselves.
Here's an example based on Pattern formation during regeneration in planaria.

This is an approach that views experiment as the primary focus of science whereas I tend to see science as a much broader way of knowing. The C.R.E.A.T.E. approach to undergraduate education emphasizes the doing of science rather than the understanding of the results and how they fit into a bigger picture. It probably does a good job of looking at "trees" but not so good a job when it comes to seeing the "forest."

I don't know the correct balance between teaching principles, ideas, and concepts and teaching the experimental approach taken by actual research scientists in their day-to-day activities. There's no question that lab courses are extremely important but I'm quite skeptical about bringing the study of experimental techniques into the lecture courses if it take time away from the conceptual understanding of the discipline.


[Hat Tip: Sandra Porter at Discovering Biology in a Digital World: Learn how to use scientific articles in education at the C.R.E.A.T.E. June workshop]

Chris Hogue on Complexity and Evolution

 
Chris Hogue is a Canadian biochemist/bioinformatician who works on protein folding (among other things) at the National University of Singapore. He used to be a professor in my department here at the University of Toronto. I miss him, and wish he were still here.

Chris blogs at BioImplement and he has just started a new series of posts on Complexity and Evolution. His goal is to explain how human design can inform us about evolution. The idea is to refute the arguments of Intelligent Design Creationists who treat intelligent design as something mystical that's1 beyond naturalism.

Here's how Chris explains what's coming ...
The thread connecting these examples of human design is that each one is an analogy to biological evolution, from which evolution may be better understood by laypersons. Now by posting new examples like this, I realize that they may all be stolen by the “intelligent design” (ID) creationists to argue against evolution. My view on ID follows that most clearly expressed in the 2005 court judgment from the Pennsylvania Kitzmiller v. Dover case: “The overwhelming evidence at trial established that ID is a religious view, a mere re-labeling of creationism, and not a scientific theory.” Of course a few scientists have written in defense of evolution and against ID nonsense in the classroom, the most strident of whom is Richard Dawkins. I now add my voice in support, as in his final interview with Dawkins, Christopher Hitchens lamented “It’s the shame of your colleagues that they don’t form ranks and say, ‘Listen, we’re going to defend our colleagues from these appalling and obfuscating elements.’”

So into the breach, I add my voice with some new arguments, after this small bit of throat-clearing. I will try to avoid being derivative as I come armed with my own capacity for inquiry, insight, and argument. My examples will show how ID concepts force the gerrymandering of human design history, and surround it with mystical borders to make their claims. The individual steps in human design are small, slow and absolutely require the intellectual imprinting of lessons by trial and error. Students who are led to think falsely about human design, or any complexity as having mystical origins are harmed by the diminishment of their own aspirations of creativity. We all need to understand how small steps and tools lead to human creativity and any object of complexity. I will reveal these small steps and show, where I can, the failures that led to success.
I know Chris and I can assure you that his upcoming posts will be provocative and informative.




Friday, January 06, 2012

Plant microRNAs in Your Blood?

 
Last month the science magazines and websites were all talking about a paper by Zhang et al. (2012) published in Cell Research. These workers discovered plant micoRNAs in the serum of mice and humans. The microRNAs seem to come from ingested rice. Presumably the micoRNAs are taken up in the intestine and secreted into the blood in small vesicles. The concentration of the major rice miRNAs in serum is about 10 fM or 10×10-15 moles per liter.1

The authors have shown that microRNA MI168a binds to the mRNA of low-density lipoprotein receptor adapter protein 1, inhibiting translation. This leads to the idea that ingested plant microRNAs can regulate the expression of human genes. That's the story that generated the most press [What You Eat Affects Your Genes: RNA from Rice Can Survive Digestion and Alter Gene Expression, Food We Eat Might Control Our Genes].

This is one of those findings where the explanation doesn't make a lot of sense but the data seem sound. It seems very unlikely that small plant RNAs could survive the processing and digestion of rice or any other food and even less likely that they would find their way into the bloodstream where they could play a role in regulating mammalian gene expression. I think I'll wait for confirmation.

It's a shame that none of the articles in the popular press expressed any sort of skepticism. That's one of the problems with science journalism. How do you convey the idea that all scientific results are preliminary until they have been confirmed by others?


1. That concentration is far below the concentration where effective binding can occur but the idea seems to be that the micoRNAs are contained in small vesicles that subsequently fuse with liver cells and deliver the rice microRNA to the cytoplasm where it can inhibit translation of specific mammalian RNAs. It's difficult to see how one could get an effective concentration of plant microRNA in one of these mammalian cells.

Zhang, L., Hou, D., Chen, X., Li, D., Zhu, L., Zhang, Y., Li, J., Bian, Z., Liang, X., Cai, X., Yin, Y., Wang, C., Zhang, T., Zhu, D., Zhang, D., Xu, J., Chen, Q., Ba, Y., Liu, J., Wang, Q., Chen, J., Wang, J., Wang, M., Zhang, Q., Zhang, J., Zen, K., and Zhang, CY. (2012) Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research 22:107–126 [PubMed] [doi:10.1038/cr.2011.158]

An important correction to several of the figures in this paper has also been published.

Zhang et al. (2012) Corrigendum [doi:10.1038/cr.2011.174]