God and Evolution (2nd notice)

 
This is the second notice of God and Evolution, a talk about the effect of intelligent design on our education system. The lectures are in my building. I'm going. Email me if you want to meet for dinner before it starts. Several people have signed up already. You can buy tickets at the door.

The lectures are sponsored by the Centre for Inquiry, Ontario [see Standing Room Only].


Brian Alters

Dan Brooks

Mushrooms for Dinner

Julia was fed up with her husband. He was cruel and abusive and obviously preferred his own son by a previous marriage to her own son by a previous marriage. They were fighting constantly and he was heard complaining about his wife to his friends and threatening to divorce her.

She couldn't let that happen. It would mean a huge change in lifestyle. Julia decided to poison her husband by serving him mushrooms for dinner. She choose the "delicacy" Amanita phalloides because it was known to act quickly. By dawn the following day, her husband was dead.

Julia's husband was Tiberius Claudius Caesar Augustus Germanicus, Emperor of Rome, and the date was October 13, 54. Julia, better known as Julia Agrippina or Agrippina the Younger, moved quickly to install her son, Nero Claudius Caesar Augustus Germanicus on the throne.

Some mushrooms of the genus Amanita contain a deady poison called α-amanitin [Monday's Molecule #18: thanks to Matt for being the first to name the molecule]. α-amanitin is a potent inhibitor of eukaryotic RNA polymerase thus blocking transcription and preventing the expression of essential genes.

The story may not be true. Nobody knows for certain that Claudius was poisoned but by all acounts it seems likely. Nobody knows for certain that Agrippina prepared the meal herself but it seems very likely she was behind the assassination.

The story has entered the list of tales told in biochemistry class because it illustrates the importance of α-amanitin. It's rarely repeated in textbooks because of the historical uncertainties, but there's a famous telling of the tale in an earlier edition of Modern Biology by Postlethwait and Hopson. On page 229 they have a Box titled Caesar Experiments with RNA Synthesis,

For the first ten hours after Casear ate this delicacy, all seemed well. But as he digested the fungus, the α-amanitin entered his bloodstream and was absorbed by his liver and kidneys, where it began to block transcription. About 15 hours after his repast, with no new mRNA to make new proteins Caesar's liver cells stopped functioning, and nausea, diarrhea, and delirium began to hit him. Two days later, he died of liver failure. It is highly doubtful that Caesar learned to appreciate the valuable role of RNA polymerase in DNA transcription. But perhaps, in a general way, Agrippina did.

How's It Working So Far in Iraq?

 
ABC News reports on the latest poll results from Iraq [Voices From Iraq 2007: Ebbing Hope in a Landscape of Loss].

Violence is the cause, its reach vast. Eighty percent of Iraqis report attacks nearby — car bombs, snipers, kidnappings, armed forces fighting each other or abusing civilians. It's worst by far in the capital of Baghdad, but by no means confined there.

The personal toll is enormous. More than half of Iraqis, 53 percent, have a close friend or relative who's been hurt or killed in the current violence. One in six says someone in their own household has been harmed. Eighty-six percent worry about a loved one being hurt; two-thirds worry deeply. Huge numbers limit their daily activities to minimize risk. Seven in 10 report multiple signs of traumatic stress.

And how do they feel about the troops who are there to help them?

The survey's results are deeply distressing from an American perspective as well: The number of Iraqis who call it "acceptable" to attack U.S. and coalition forces, 17 percent in early 2004, has tripled to 51 percent now, led by near unanimity among Sunni Arabs. And 78 percent of Iraqis now oppose the presence of U.S. forces on their soil, though far fewer favor an immediate pullout.

That's not a good sign. But at least they're better off than they were under Saddam Hussein, right?

Given all this, for the first time since the 2003 war, fewer than half of Iraqis, 42 percent, say life is better now than it was under Saddam Hussein, whose security forces are said to have murdered more than a million Iraqis.

Forty-two percent think their country is in a civil war; 24 percent more think one is likely. Barely more than four in 10 expect a better life for their children.

Three in 10 say they'd leave Iraq if they could.

It's time for the foreign troops to leave. Get out as fast as possible.

[Hat Tip: Canadian Cynic]

Transcription

 
Transcription is the process where a gene (DNA) is copied into single-stranded RNA. The enzyme responsible for this process is called RNA polymerase. (DNA polymerase is the enzyme that copies DNA during DNA replication. They are very different enzymes even though they carry out similar reactions.)

Transcription can be divided into three steps: initiation, elongation, and termination. It's easiest to describe the process in bacteria because it's simpler than eukaryotic transcription. The basics are the same in all species.

The bacterial enzyme is called the RNA polymerase holoenzyme because it's actually a complex of RNA polymerase and an activator protein. The initiation step involves assembling a transcription initiation complex at the beginning of the gene. The site of initiation is called the promoter.

The first thing that happens is that RNA polymerase binds to any old sequence of DNA then it slides along the DNA looking for a promoter sequence. The non-specific binding of E. coli RNA polymerase holoenzyme is weak and it dissociates after about three seconds. However, during that time it can slide about 2000 base pairs looking for a promoter sequence. This one-dimensional search allows it to find the start of a gene and initiate transcription much more quickly than if it had to bind directly to a promoter.

Promoters have specific DNA sequences that are recognized by the activator protein. Recall that the activator protein is part of the hololenzyme complex. In E. coli the bound activators are called σ (sigma) factors. Different σ factors recognize different promoters. In other species the activator proteins may bind to the promoter first and the RNA polymerase will encounter it when it slides along DNA. The net effect is the same whether the activator binds first to DNA or to the promoter: a transcription initiation complex assembles at the promoter.
The actual initiation event requires opening the double-stranded DNA to make a transcription bubble. Then the first few nucleotides of RNA are synthesized by copying one of the strands of DNA.

At this point the activator protein releases the RNA polymerase, which is now tightly bound to the transcription bubble. Various elongation factors join the complex and transcription proceeds along the gene copying one of the strands into RNA. As the complex moves the RNA unwinds behind the RNA polymerase and the DNA reforms a double helix. The transcription bubble moves along the gene. In the example shown below the major elongation factor (NusA) is binding to RNA polymerase as the σ factor is ejected.

Note that the shift from initiation complex to elongation complex is a crucial step in initiation. The activation protein is tightly bound to the promoter and the complex would not be able to leave the promoter if it didn't dissociate from the activator protein (σ factor, in the case of E. coli).

At the end of the gene, the elongation complex encounters a specific termination signal where specific termination factors catalyze the dissociation of RNA polymerase from DNA and the completed RNA is released.

Whether or not a gene is transcribed depends on the promoter sequence. If there's an activator protein in the cell that binds to that promoter then the gene will be transcribed. The rate of transcription will depend on how much of the activator protein is present because the more activator there is the more quickly it will find and bind to the promoter.

The rate of transcription will also depend on the strength of the promoter. If the promoter sequence is a perfect match to the ideal binding site of the activator then the gene will be transcribed often. On the other hand, if the promoter sequence is similar to the ideal binding site but not a perfect match then it will be transcribed less often because the activator won't bind as tightly. Selection will favor the appropriate promoter strength—not all promoters are ideal binding sites because not all genes need to be transcribed at maximum rate.

Gene and Transcription Orientation

 
The DNA double helix consists of two strands of DNA wound around each other to form the classic helical structure. One of the most important insights into solving the structure was when Watson and Crick realized that the two strands had to run in opposite direction. The ends of each strand are identified by the carbon atom on the deoxyribose sugar. One end is called the 5′ (five prime) end because the 5′ carbon atom is exposed. The other end is called the 3′ (three prime) end because the 3′ carbon atom is exposed.

RNA (and DNA) can only be synthesized from the 5′ to the 3′ direction. What this means is that at the beginning of the gene when the transcription bubble forms it's the template strand that's copied into RNA and the beginning of the template strand is the 3′ end. (It's the opposite orientation of the newly synthesized RNA.) [see Transcription]

The complementary strand of DNA is called the coding strand because it represents the sequence of the gene product. In other words, it's the same sequence as the RNA. By convention the orientation of the gene is determined by the coding strand and not the template strand. Thus, the beginning of a gene is called the 5′ end and the end of a gene is the 3′ end;.

The electron micrograph below shows E. coli ribosomal RNA genes being transcribed. The thin line (upper right) is the Double-stranded DNA strand. Transcription of the genes begins at the initiation site (lower left). This is the 5′ end of the genes.

RNA polymerase first bound to the initiation site and began transcribing in the 5′ to 3′ direction as shown. As the transcription complex moves along the gene the RNA product gets longer. In this case it is bound to protein so it looks compact. About halfway along the genes the RNA is processed by cutting and that's why it seems to get shorter near the middle of the gene.

The large ribosomal RNA is in the second half of the transcribed region. You can see that the RNA in the second half is larger than the small ribosomal RNA in the first half.

Note that there are many transcription complexes transcribing this region at the same time. In fact, they are about as closely packed as they can possibly be. These genes are being transcribed at the maximum possible rate. They have a very strong promoter.

Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome

In April 2005 Gil Ast published an article in Scientific American (Ast, 2005). The title of the article was “The Alternative Genome” and its main point was how alternative splicing in humans could increase the number of different proteins that we produce. He explains why he thinks the proteome is so much larger than the number of genes. (Ast claims that there are 90,000 proteins and only 25,000 genes.)

Ast begins his argument with the quotation below.

Spring of 2000 found molecular biologists placing dollar bets. Trying to predict the number of genes that would be found in the human genome when the sequence of its DNA nucleotides was completed. Estimates at the time ranges as high as 153,000. ... given our complexity we ought to have a bigger genetic assortment than the 1000-cell roundworm, Caenorhabditis elegans, which has a 19,500-gene complement, or corn, with its 40,000 genes.

When a first draft of the human sequence was published the following summer, some observers were therefore shocked by the sequencing team’s calculation of 30,000 to 35,000 protein-coding genes. The low number seemed almost embarrassing.

Ast's remarks illustrate two points that I want to address. The first point is the surprise factor. Ast, and some other scientists, were surprised (and embarrassed) by the low gene count. They imply that most genome experts were also shocked when the genome sequence was published. That’s not quite correct, as I will show below.

The second point will have to be put off for another time but it’s important enough to mention here. Ast thinks that humans need to make many times more proteins than worms and corn because we are so much more complex. There are two problems with such a point of view—are we, in fact, 2-3 times more complex than corn? And, does it take thousands of new proteins to generate the structures that make us unique?

I think some people exaggerate our complexity and the place of humans relative to other species. This incorrect perspective can cause some scientists to put their faith in weakly supported hypotheses that claim to explain why humans really are complex and important in spite of the fact that we don’t have a lot of genes.

But let's put that discussion aside for a few days in order to discuss the historic estimates of the number of genes in the human genome. The statement by Gil Ast is typical of those who are embarrassed. They exaggerate the estimates of the total number of genes in order to make it look like everyone—not just them—thought there would be far more genes than the 25,000 that have been found. Just this month (March 2007) this myth was repeated by Taft et al. (2007).

Predictions of the estimated number of protein-coding genes in the human genome prior to genome sequencing ranged from as low as 50,000 to as high as 140,000, whereas the latest estimates from genome analysis indicate that humans have approximately 20,000 protein-coding genes.

The graphic above was taken from the Genesweep lottery. This is the betting that Asp refers to. It shows the range of gene number estimates by scientists who were involved in genome sequencing projects. Note that there are many estimates in the 40-50,000 range and a fair number below 40,000. The point is obvious—lots of experts anticipated fewer than 50,000 genes in the human genome (see The nature of the number. Nature Genetics 25:127 (2000)).

The earliest estimates of gene number are based on genetic load arguments (see King & Jukes, 1969). Since approximate mutation rates were known by 1960, it was possible to estimate the maximum number of genes that could be mutated without presenting an impossible genetic load. In other words, how many genes could we have before the number of lethal mutations per generation became intolerable? This number was less than 40,000 genes; an estimate that has never been refuted or discredited. Many experts were well aware of this upper bound up until the time the genome sequence was published.

By the 1970's there were good estimates of the total number of unique Drosophila melanogaster genes that could be mutated to lethality. The range was about 5,000-10,000 genes and this correlated well with the genetic map and the organization of polytene chromosomes. It was known that the Drosophila genome was much larger than the total size of the estimated number of genes but studies from a number of labs confirmed that a great deal of genomic DNA was repetitive junk DNA.

As we learned more and more about how genes controlled development, it became clear that huge differences in morphology and "complexity" could be due to very small changes in the either the number of regulatory genes or when they were expressed. Most of the people who assimilated the advances in developmental biology began to appreciate that mammals do not need to have many more genes than fruit flies.

By 1980, the amount of unique sequence DNA in mammalian genomes was known to be capable of encoding fewer than 20,000 genes if the average size of a gene was 10,000 bp (including introns). We now know that much of the intron sequences is not unique sequence DNA but that wasn't known back then. This estimate of gene number was consistent with detailed analysis of the amount of DNA that could be protected by mRNA or by Rot analysis (kinetics of hybridization of RNA to DNA). Mouse embryos (gastrula) appeared to express about 20,000 average-sized mRNAs. Some of these were present at very low abundance leading to the idea that this value may represent most of the mouse genes in the genome (summarized in Lewin, 1980). Certainly it was known that mammals expressed about 10,000 housekeeping genes in most cells and tissues. The general consensus was that the total number of regulatory genes was unlikely to be more than twice this number (probably less) for a total of 30,000 genes at most.

It was about this time that Walter Gilbert made his famous back-of-the-envelope calculation of 100,000 genes in the human genome. This was the estimate that became widely quoted when the human genome project was first proposed. It's interesting to note that Gilbert's estimate was not based on any experimental evidence; indeed, it conflicted with most of the available evidence suggesting far fewer genes. The larger number seemed less threatening to scientists who were worried that we might not have more genes than a fruit fly.

By the late-1990's we had estimates of the total number of human genes from the sequences of chromosomes 21 and 22 and from the sequence of a large contiguous region of the MHC locus. The results suggested fewer than 45,000 genes total—even less if these sequenced regions turned out to be gene rich as was widely suspected. Thus, the number of genes was coming out to be well below 50,000 and this was in line with the data from RNA hybridization studies and genetic load. It also fit with the concept that the number of genes in mammals was probably not more than twice the number in insects.

In contrast to these results, the estimates from expressed sequence tags (ESTs) were often much higher. Expressed sequence tags are short copies of RNA isolated directly from cells. The idea was that these represented bits of mRNA so each one revealed the presence of a protein-coding gene. As more and more ESTs were deposited in the sequence libraries, it became possible to estimate when the library would be complete and the totals were often more than 100,000 distinct mRNAs. For example, just before the human genome sequence was published, (Liang et al., 2000) estimated that there were 120,000 genes based on the analysis of 2 million EST's.

Not everyone believed in the validity of the EST data. There were some who thought that most ESTs were artifacts. They turned out to be correct although this is not widely appreciated. By using the sequences of chromosomes 21 and 22 as controls Ewing and Green (2000) were able to estimate 35,000 genes based on the EST libraries.

Thus, by the time the draft sequence was published in 2001 there were many scientists who anticipated that the number of genes would be less than 40,000 and that's why there are so many bets in that range in the Genesweep lottery. When the number of genes was announced to be about 30,000 there were many of us who were not the least bit surprised. The only ones who were surprised were those who ignored most of the data and clung to the idea humans had to have far more genes than the so-called "lower" species.

It is simply not true that all the experts were surprised at the low number of genes. Some experts were, but many were not. The interesting thing is that those who wanted there to be more genes have not given up the fight. They continue to publish rationalizations and just-so stories in an attempt to justify why they were wrong.

UPDATE:The latest estimates indicate that the human genome contains about 20,500 protein-encoding genes [Humans Have Only 20,500 Protein-Encoding Genes]. There are probably about 1500 genes for the known stable RNAs for a total of 22,000.

Ast,G. (2005) The alternative genome. Sci. Am. 292; 40-47.

Ewing,B. and Green,P. (2000) Analysis of expressed sequence tags indicates 35,000 human genes. Nat. Genet. 25; 232-234.

King,J.L. and Jukes,T.H. (1969) Non-Darwinian evolution. Science 164; 788-798.

Lewin, B. (1980) Gene Expression-2 2nd ed. Chapter 24; Complexity of mRNA Populations.

Liang,F., Holt,I., Pertea,G., Karamycheva,S., Salzberg,S.L., and Quackenbush,J. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat. Genet. 25; 239-240.

What Is This?

 
Why it's Stenocereus eruca, of course.

Don't know what that is?

Find out if it's a plant, an animal, or something else entirely by going [here].

It (mostly) doesn't have sex but shows a fairly high level of genetic diversity.

Sex, genes & evolution

 
With a title like that how could you not want to read John Logsdon's new blog? Yesterday was his first post but I'm looking forward to lots more in the near future [Sex, Genes & Evolution].

John is a molecular evolutionary biologist in the Biology Department at the University of Iowa. He has published a number of papers with W. Ford Doolittle from the time he was at Dalhousie University in Nova Scotia. These include several papers with Arlin Stoltzfus on the evolution of introns. The Stoltzfus/Logsdon papers from this era were among the best papers to refute the intron-early hypothesis formerly championed by their mentor, Ford Doolittle. One of the things this demonstrates is that it's possible to disagree with your boss and survive!

Their chief target at the time was the Gilbert lab. John Logsdon was one of the participants in the famous online BioMedNet debate on The Origin and Evolution of Introns in November 1996—back in the time before blogs. This was mostly a debate between members of the Ford Doolittle lab and the Gilbert lab. Unfortunately, the transcript is no longer available. It was required reading in most molecular biology courses in the late 1990's. (I wish we had more debates like that.)

The Logsdon lab is interested in sex in protists, specifically the evolution of genes involved in recombination and meiosis (e.g., RAD51). John participates in a larger project that is trying to define the eukaryotic tree of life. As most of you know, the relationship of protists is controversial and the collaborative project intends to try and resolve the controversies. It not going to be easy to figure out the early history of eukaryotic evolution. This is a problem that has perplexed evolutionary biologists for several decades.

The Iowa biologists' goal is to sequence nine genes (actin, α- and β- tubulin, cob, EF-1 a , Hsp70, Hsp90, RPB1, SSU rRNA) from at least 200 different protists [ Assembling the Tree of Eukaryotic Microbial Diversity and Eu-Tree].

I'm excited about this project because they're looking at the best gene (HSP70). I hope he won't be disappointed to learn that my undergraduates have already solved the problem [The Evolution of the HSP70 Gene Family]. But all is not lost, those other genes might make a minor contribution to understanding evolution.

Welcome to science blogging, John.

Now, why not jump right in and describe your favorite hypothesis for why we have sex? I'm guessing you're a fan of repair, right?

Monday's Molecule #18

 
Name this molecule. You must be specific but we don't need the full correct scientific name. (If you know it then please post it.)

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. This one's very easy once you know the molecule. There'll be a few extra bonus points for guessing Wednesday's Nobel Laureate(s).

Comments will be blocked for 24 hours. Comments are now open.

How Nerdy Am I?

 



[Hat Tip: Shalini.]

What Color Green Am I?

 

You Are Emerald Green

Deep and mysterious, it often seems like no one truly gets you. Inside, you are very emotional and moody - though you don't let it show. People usually have a strong reaction to you... profound love or deep hate. But you can even get those who hate you to come around. There's something naturally harmonious about you.

What Color Green Are You?

[Hat Tip: Monado]

A New Transitional Fossil

 
This is a new transitional fossil manmmal called Yanoconodon. It's from the Meozoic era (about 200 million years ago). The fossil tells us a great deal about mammalian evolution, especially the evolution of the jaw and ears. If you are interested in evolution you must read PZ Myers' excellent description of this fossil [Yanoconodon, a transitional fossil].

The creationist and intelligent design websites will soon be out with their own explanation of how this fossil fits with their version of the history of life. I'll link to them as soon as they post. If you spot these interpretations before I do, please let me know. I can't wait to see how they handle this news scientific evidence.

Meanwhile, congratulations PZ for a wonderful article.

Intelligent Design for Dummies

 
Do you understand Intelligent Design? Fear not, UK comedian Robin Ince explains it in a clip from the show "Comedy Cuts" aired March 15th on ITV in the UK. (Why can't there be more documentaries like this on TV in the USA?)



[Hat Tip: PZ Myers.]

Stéphane Dion Does Milton

 
Jennifer Smith has all the details over at Runesmith's Canadian Content [Dion Does Milton].

Sounds like it was a lot of fun. I hope he comes to my riding. It was the one formerly represented by Carolyn Parrish. But she was kicked out of the Liberal party so that's not quite the same as supporting a new Liberal like Garth Turner.

Happy St. Patricks Day!!!

 

Today's the day when the Irish—and people who want to be Irish—celebrate by doing typically Irish things; like drinking green beer, dancing Irish jigs, and going to mass. (?)

My ancestors on my mother's side are (mostly) Irish. My grandfather was a Doherty (O'Doherty). Thats the name at the top of the map in country Donegal. That side of the family came to Canada in 1802 and the Irish blood has been diluted—most notably by American refugees from the Revolutionary War (United Empire Loyalists) (gasp!).

The O'Doherty's are descended from Niall Noigíallach who kidnapped St. Patrick.

My grandmother was a Foster from Fermanagh. That's by the two lakes (Lower Lough Erne and Upper Lough Erne) in the upper central part of the country near the seat of the Maguires. Her family came to Canada in 1865 but both of her parents were Irish so at least 1/4 of my genes are undiluted Irish. I'll drink to that.

We don't talk about the nasty little fact that the Foster's were probably English invaders from the 1600's. As they say, somebody had to civilize the Irish and it might as well have been the English!

One of the reasons why the topic was avoided by my grandparents was because the O'Doherty clan was almost wiped out by the English during the O'Doherty rebellion in 1608 led by Sir Cahir O’Doherty. Some of the survivors had to flee to Skye to avoid being hung. I descend from those refugees.