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.

Roundup® Is Safe

There have been dozens of studies on the possible harmful effects of Roundup®. There are many well-funded organizations and tons of lawyers who would like nothing better than to sue Monsanto into bankruptcy. Given the millions of farmers and suburban gardeners who slop Roundup® on themselves on a regular basis, you'd think it would be easy to come up with some who have died of cancer or, at least, suffered serious health problems.

Hasn't happened. Most of the scientific studies find no harmful effects of Roundup® on humans. Here's a bit from a study done for THE COMMONWEALTH OF MASSACHUSETTS in 2003.

TOXICITY REVIEW
Acute (Mammalian)
Glyphosate has reported oral LD5Os of 4,320 and 5,600 mg/kg in male and female rats (15,4). The oral LD5Os of the two major glyphosate products Rodeo and Roundup are 5,000 and 5,400 mg/kg in the rat (15). A dermal LD5O of 7,940 mg/kg has been determined in rabbits (15,4). There are reports of mild dermal irritation in rabbits (6), moderate eye irritation in rabbits (7), and possible phototoxicity in humans (9). The product involved in the phototoxicity study was Tumbleweed marketed by Murphys Limited UK (9). Maibach (1986) investigated the irritant and the photo irritant responses in individuals exposed to Roundup (41% glyphosate, water, and surfactant); Pinesol liquid, Johnson Baby Shampoo, and Ivory Liquid dishwashing detergent. The conclusion drawn was that glyphosate has less irritant potential than the Pinesol or the Ivory dishwashing liquid (120).
Metabolism
Elimination of glyphosate is rapid and very little of the material is metabolized (6,106).
Subchronic/Chronic Studies (Mammalian)
In subchronic tests, glyphosate was administered in the diet to dogs and rats at 200, 600, and 2,000 ppm for 90 days. A variety of toxicological endpoints were evaluated with no significant abnormalities reported (15,10). In other subchronic tests, rats received 0, 1,000, 5,000, or 20,000 ppm (57, 286, 1143 mg/kg) in the diet for 3 months. The no observable adverse effect level (NOAEL) was 20,000 ppm (1,143 mg/kg) (115). In the one year oral dog study, dogs received 20, 100, and 500 mg/kg/day. The no observable effect level (NOEL) was 500 mg/kg (116).

etc.

You may not like Monsanto and genetically-modified food for ethical reasons or because the company exploits third-world farmers. These are valid, if controversial, reasons for opposing the spread of genetically-modified crops. Personally I don't have a problem with genetically modified foods, but I do have a problem with the power of large international for-profit companies.

Express your opposition, if it's rational and scientifically based, but don't fall into the trap of opposing GM foods because you think Roundup® is dangerous. This kind of opposition (see below) is just plain silly. It is a superstitious, anti-science, way of thinking.

If You Think Monsanto's Roundup is a Safer Pesticide,
Please read the articles and papers on this page! Roundup is a pesticide as defined by the EPA.

If you're still not convinced that Roundup is a highly toxic and persistent pesticide, read on, while at the same time remembering the other contributions that Monsanto has made to society such as:

Saccharin, Astroturf, agent orange, dioxin, sulphuric acid, polychlorinated biphenyls (PCBs), plastics and synthetic fabrics, research on uranium for the Manhattan Project that led to the construction of nuclear bombs, styrene monomer, an endless line of pesticides and herbicides (Roundup), rBGH (recombinant bovine growth hormone that makes cows ill), genetically engineered crops (corn, potatoes, tomatoes, soy beans, cotton), and it's most significant product to date; Lies, Factual Distortions and Omissions.

[from Everything You Never Wanted to Know About Monsanto's Modus Operandi (M.O.)]

Glyphosate-resistant Weeds

Roundup® (glyphosate) has been used to control weeds since 1974 [How Roundup® Works]. In all those years, the number of reported cases of resistant plants has been far below predictions. Only in the past ten years have Roundup®-resistant plants been identified and there are only 11 species of resistant weeds known at last count (Perez-Jones et al. (2007).

We now know from studies of the mechanism of resistance of the C4 EPSP synthase that resistance to glyphosate requires very special circumstances; namely, an enzyme active site that can exclude glyphosate while still allowing phosphoenolpyruvate to bind efficiently [The Molecular Basis of Roundup® Resistance]. Thus, with hindsight, it is perhaps not surprising that so few resistant plants have turned up.

One of the first resistance mechanisms to be discovered was one that evolved in a population of goosegrass from Malaysia (Baerson et al. 2002). The glyphosate-resistant biotype (strain) was from a region that had been continuously sprayed for 10 years.

Baerson et al. (2007), working out of the Monsanto Labs in St. Louis MO (USA), discovered that the resistant strain of goosegrass was resistant to about five times the normal level of glyphosate. All of this resistance was apparently due to a single amino acid change in the active site of EPSP synthase. The substitution of a proline for a serine residue at position 106 decreased glyphosate binding without affecting phophoenolpyruvate binding.

Taken together, these studies suggest that an altered EPSPS provides a significant component of the glyphosate resistance mechanism in goosegrass, and represents the first example for target-based resistance to glyphosate occurring in any plant species.

The authors cannot explain why this P106S substitution confers resistance in the goosegrass enzyme, since similar substitutions in other plant enzymes affect substrate binding and render the enzyme ineffective. They conclude with,

It is possible that goosegrass may be predisposed to this type of mechanism due to species-specific genetic or physiological characteristics that remain obscure at present.

This has important implications for our understanding of evolution. Taken at face value, it suggests that in some species an evolutionary path is simply not available—there may not be a route to the so-called "top of the fitness peak." On the other hand, in other species a path can open up with a single mutation because that species, by chance, has the right kind of background. Evolution by accident.

Glyphosate-resistance has independently evolved in two strains of Italian ryegrass (Lolium multiflorum) from Oregon and Chile. The mechanism of resistance was studied by Perez-Jones et al. (2007). In this case there are two different mechanisms of resistance.

The strain from Chile had the same EPSP synthase mutation as that found in goosegrass (proline for serine at position 106). The Orgeon strain was defective in absorbing glyphosate in the roots suggesting a defect of some sort in absorption and/or transport. This is a new kind of resistance and it's not well understood at this time.

There have been rumors of Roundup® resistant coca plants in Bolivia—the ones whose leaves are used to produce cocaine. The rumors were so persistent that the magic crop was tested to see if it had been genetically engineered in a secret lab sponsored by the drug lords [The Mystery of the Coca Plant That Wouldn't Die]. The article reports that tests for C4 EPSP synthase were negative suggesting that the plants have acquired a natural resistance.

The implication is that the farmers' decentralized system of disseminating coca cuttings has been amazingly effective - more so than genetic engineering could hope to be. When one plant somewhere in the country demonstrated tolerance to glyphosate, cuttings were made and passed on to dealers and farmers, who could sell them quickly to farmers hoping to withstand the spraying. The best of the next generation was once again used for cuttings and distributed.

This technique - applied over four years - is now the most likely explanation for the arrival of Boliviana negra. By spraying so much territory, the US significantly increased the odds of generating beneficial mutations. There are numerous species of coca, further increasing the diversity of possible mutations. And in the Amazonian region, nature is particularly adaptive and resilient.

"I thought [genetic engineering] was unlikely," says Gressel, the plant scientist at the Weizmann Institute. "But farmers aren't dumb. They obviously spotted a lucky mutation and propagated the hell out of it."

The effects of this are far-reaching for American policymakers: A new herbicide would work only for a limited time against such a simple but effective ad hoc network. The coca-growing community is clearly primed to take advantage of any mutations.

From what we know of glyphosate resistance it seem unlikely that these Bolivian plants are actually resistant to Roundup®. It's probably just over-active imagination.

Baerson, S.R., Rodriguez, D.J., Tran, M., Feng, Y., Biest, N.A., Dill, G.M. (2002) Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Plant Physiol. 129:1265-1275. [PubMed]

Perez-Jones, A., Park K.W., Polge, N., Colquhoun, J., and Mallory-Smith, C.A. (2007) Investigating the mechanisms of glyphosate resistance in Lolium multiflorum. Planta. 2007 Feb 24 (electronic publication, ahead of print).

Wanna Speciate? Come to Canada

A recent Science paper by Wei and Schluter (2007) asks whether speciation rates really are faster in the tropics as widely believed. They looked at 309 sister species of mammals and birds in North and South America. Sister species are closely related species that have apparently diverged within the past few million years. The time since divergence was estimated by comparing the sequences of the mitochondrial cytochrome b gene. This gives an estimate of the rate of speciation by cladogenesis for each pair of sister species.

The range of each species was estimated from literature data and the time of speciation results were plotted in relation to the midpoint latitude of the range. The result was quite striking.

Near the equator, the ages of sister-species pairs spanned the past 10 million years, with a mean age of 3.4 million years ago. As the distance from the equator increased, the upper limit and mean ages of sister species declined significantly. At the highest latitudes, all of the sister species diverged less than 1.0 Ma.

It's widely known that there are far more species in the tropics than in temperate or arctic climates. How do we explain this apparent discrepancy?

Weir and Schluter (2007) estimated extinction rates at various latitudes and discovered that the rate of species extinction also increased with distance from the equator but the rate of increase was greater than the rate of increase in speciation. Thus, although there were more speciation events in temperate zones, there were also more extinctions, and the extinctions cancelled out the effect of frequent cladogenesis.

The net effect is more species in the tropics even though speciation rates are higher in temperate zones.

John Wilkins is an expert on species. He points out that there's no universal definition of species. I wonder if this result isn't biased by different ways of recognizing species. Perhaps populations and sub-species are more easily named in temperate zones because there's more room for them to spread out into non-overlapping ranges. Does anyone know whether "species" in temperate zones are more likely to be similar in appearance than in the tropics?

In any case, the result is intriguing. It suggests that things move pretty slowly in hot climates. If you want some fast speciation action you need to move north to a cooler place.

Weir, J.T. and Schluter, S. (2007) The Latitudinal Gradient in Recent Speciation and Extinction Rates of Birds and Mammals. Science 315: 1574-1576.

[Hat Tip: RichardDawkins.net; Cold is hot in evolution -- Researchers debunk belief species evolve faster in tropics]

St. Patrick Banished Snakes from Ireland

 
Friday's Urban Legend: FALSE

Connie Barlow describes A St. Patrick's Day Parable.

Ireland is a land of no snakes. It has no slithering serpents. There are no rat snakes in Ireland; there are no rattlesnakes; there are no garter snakes. There are no snakes at all.

The absence of snakes in Ireland seems to cry out for an explanation — but only if one regards or ventures to the island from outside: from England, say, or from continental Europe. To the indigenous Celts, there would, of course, have been nothing to explain. The Gaelic peoples no more needed to explain an absence of snakes on their island home than they needed to explain an absence of kangaroos. To those who came to Ireland from abroad, however, a dearth of serpents was a striking anomaly in need of an answer.

We humans must have answers. And so arose the legend of St. Patrick and the snakes. The reason Ireland has no snakes, the story goes, is that Patrick charmed all snakes on the island to come down to the seashore, slither into the water, and drown. So Ireland did once have snakes, but it has them no more. Patrick charmed them all into the sea.

She goes on to explain why there are no snakes in Ireland but I prefer to swtich to the website of the Smithsonian National Zoological Park for their explanation of Why Ireland Has No Snakes.

Now snakes are found in deserts, grasslands, forests, mountains, and even oceans virtually everywhere around the world. Everywhere except Ireland, New Zealand, Iceland, Greenland, and Antarctica, that is.

One thing these few snake-less parts of the world have in common is that they are surrounded by water. New Zealand, for instance, split off from Australia and Asia before snakes ever evolved. So far, no serpent has successfully migrated across the open ocean to a new terrestrial home. As the world's oceans have risen and fallen over the millennia, land bridges have come and gone between Ireland, other parts of Great Britain, and the European mainland, allowing animals and early humans to cross. However, any snake that may have slithered it's way to Ireland would have turned into a popsicle when the ice ages hit.

The most recent ice age began about three million years ago and continues into the present. Between warm periods like the current climate, glaciers have advanced and retreated more than 20 times, often completely blanketing Ireland with ice. Snakes, being cold-blooded animals, simply aren't able to survive in areas where the ground is frozen year round. Ireland thawed out for the last time only 15,000 years ago. Since then, 12 miles of icy-cold water in the Northern Channel have separated Ireland from neighboring Scotland, which does harbor a few species of snakes. There are no snakes in Ireland for the simple reason that they can't get there.

[The book cover is from a book by Sheila MacGill Callahan (Author) and Will Hillenbrand (Illustrator). You can buy it on Amazon.com.]

War is Not Healthy for Children and Other Living Things

For the longest time we had a poster on our wall that said "War Is Not Healthy for Children and Other Living things" [War Is Not Healthy: The True Story].

The sentence seems trite if you didn't live though the 60's but it's taking on more and more significance every day. The point is that war is hell. People die. Innocent people. We better not forget that.

But there are people who do want to forget. They want to purge war of all of it's ugliness and remember only the bravery and the glory. In Canada the movement to glorify a deadly First World War battle—the battle of Vimy Ridge—is gaining ground. In this battle there were 30,000 casualties and the front advanced a few miles. There was no strategic gain. This was a war that should not have happened and a battle that wasted thousands of lives. It was not glorious and it should be something to be embarrassed about, not celebrated.

But there's an even more important illustration of our tendency to forget the horrors and the mistakes of war. Tuesday's Globe and Mail has an article about veterans protesting a sign at the Canadian War Museum in Ottawa. The issue concerns strategic bombing in World War II and it's a hot button issue in Canada because of a documentary televised several years ago.

The goal of Bomber Command during World War II was to destroy German cities and reduce Germany's will to continue the war. Nobody was under any illusions about the consequences because London and other British cities had been bombed in 1940. They knew that flower gardens would be wiped out and so would little children [Strategic bombing during World War II]. The image below is of bombed out apartment buildings in Hamburg in 1944. People used to live in those buildings. Thousands and thousands died during the firestorms created by massive bombing raids by British and American forces during 1944 and 1945.

These are facts. The controversy is about whether the bombing raids were effective. There are many who say they weren't; in fact, there seems to be a consensus among historians that strategic bombing of Germany did not have as much negative effect as the High Command believed.

Thousands of Allied airmen died in planes over Germany. Many of them were Canadians. The Canadian War Museum has a display dedicated to those airman. I have seen it. I have shown it to my children. My father was a pilot during World War II.

There are plaques and pictures describing the planes and the crews. One of the plaques is titled An Enduring Controversy. It reads,

The value and morality of the strategic bombing offensive against Germany remains contested. Bomber Command's aim was to crush civilian morale and force Germany to surrender by destroying its cities and industrial installations.

Although Bomber Command and the American attacks left 600,000 Germans dead and more than five million homeless, the raids resulted in only a small reduction in German war production until late in the war.

This is what the controversy is all about. The Royal Canadian Legion objects to this plague because it calls into to question the morality of strategic bombing and the morality of bomber crews who served during World War II.

Last year, the veterans complained that the panel made them look like war criminals. Art Smith, a veteran leading the attack, said, "Ten thousand crewmen didn't make it back. It really distresses me that people want to knock their memory." A former member of Parliament, he lobbied for a private member's bill to force a rewrite of the text.

Guess what? War is hell. War is immoral. You can't pretty it up by ignoring the truth. Bombs killed women and children. Lots of them. Their lives may have been wasted because nothing was gained by their deaths.

We owe it to our sons and daughters to leave that plaque just the way it is. We need to remind them that war isn't healthy for children and other living things. The children of Iraq and Afghanistan know this.

The Web of Life

Regular readers of Sandwalk will recall a series of articles on the death of the Three Domain Hypothesis. One of them covered the ideas of W. Ford Doolittle from Dalhousie University in Nova Scotia [If the Tree of Life Fell, Would We Recognize the Sound?]. He advocates a web of life with numerous exchanges of genes during the early years.

The figure below is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American


Doolittle has a new paper out in PNAS (Doolittle and Bapteste, 2007). In that paper he restates his ideas about the web of life and emphasizes the fact that most of us are making unsubstantiated assumptions about the treelike structure of life. This is not a criticism of evolution—far from it—but as you might expect it has attracted the attention of anti-science writers such as Casey Luskin.

Doolittle and Bapteste (2007) are opposed to the bifurcating tree of life such as the one shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes]. They say,

The meaning, role in biology, and support in evidence of the universal "Tree of Life" (TOL) are currently in dispute. Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life's earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse.

The argument is long and complex but the essence is that we need to abandon our assumption that the tree of life can be represented by: (i) a unique hierarchical pattern, (ii) the historical record can be best represented by a branching pattern, and (iii) natural selection is the primary cause of speciation.

We've pretty much abandoned the third point ...

As to this third possibility, modern evolutionists accept the uncoupling of selection from divergence, not only at the molecular level (the neutral theory) but in certain models for speciation, without seeing the Darwinian (or at least the neo-Darwinian) theory as refuted (21, 22). We have come to appreciate the plurality of evolutionary processes of lineage diversification. But most of us hold on to the first two tenets, that there is a real and universal natural hierarchy, and that descent with modification explains it, in much the same way as Darwin did. We may be process pluralists, but we remain pattern monists.

This brings us to the title of their paper Pattern Pluralism and the Tree of Life Hypothesis. Doolittle and Bapsiste want us to not only be pluralists with respect to the mechanism of evolution but also with respect to the pattern of evolution.

Doolittle maintains that lateral gene transfer (LGT) is so common that it's impossible to construct a reliable bifurcating tree to represent the actual history of life. In other words, a Tree of Life is not only technically difficult but impossible in theory as well. This problem extends to all branches of the prokaryotic tree including the major divisions. Even the existence of two prokaryotic domains is questionable. Rooting the tree of life is out of the question.

I'm a big fan of Ford Doolittle—after all, he's an honorary Canadian! I certainly agree with him about the demise of the Three Domain Hypothesis. (Most people seem to have missed the death announcement.) I also agree with him that early evolution is more like a web of life than a tree of life. Nevertheless, I think he goes too far. Lateral gene transfer is an important, and common, phenomenon but I don't think it's quite as prevalent as he makes out. I still think that a bifurcating tree can be used to represent most species evolution after about 2.5 billion years ago.

Doolittle, W.F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. (USA) 104:2043-2049. [PubMed]

More on Cellphones in Hospitals and How Doctors Deal with Evidence

 
Last Friday I mentioned a study done at the Mayo Clinic where they looked at the practice of banning cellphone use in hospitals [Cell Phones Can Cause Death in Hospitals]. The study concluded that there is no scientific evidence to support such a ban. Cellphones and BlackBerry's do not interfere with hospital equipment, according to the study.

Tuesday's Globe and Mail had a skeptical front page article on banning cellphones in hospitals [Hole Poked in Hospital Cellphone Shroud].

Cellphone use does not interfere with medical equipment and should be allowed in hospitals, according to a study that turns years of warnings on its head.

The study comes amid a sharp debate within the medical profession, with some institutions beginning to loosen their rules while others stick to the view that the devices can be dangerous to patients.

Among the people interviewed was Chris O'Conner at Mississauga Trillium Health Centre. This large teaching hospital is part of the University of Toronto Medical School. It's my local hospital and I've been there many times, both as a patient and a visitor.

Trillium lifted their ban on cellphones two years ago. Not only that, the staff is encouraged to communicate with each other using BlackBerrys and other devices. According to O'Conner, this has not only improved efficiency but also enhanced patient safety by avoiding communications lapses.

So, why are cellphones banned at other hospitals? Is this a problem? I don't know whether you could say the ban is a serious "problem," but it sure is an inconvenience. For parents sitting in an emergency waiting room for 6 hours it is frustrating to have to rely on a pay phone to keep others informed of what's happening. For those of us who are picking up someone from a hospital, it is annoying to not know when a patient is about to be discharged. (We recently had to pick up a patient from a large downtown teaching hospital. Fortunately they don't ban cellphones so we were able to keep in touch with the patient and find out when he was going to be released.) For patients in a hospital bed it is sad that they can't use their cellphones to talk to friends and relatives.

These concerns are real enough but my main interest is the conflict between rationalism and superstition. The Globe and Mail also interviewed spokeswoman Brandy Delves from a major Vancouver hospital.

A spokeswoman for Vancouver Coastal Health said last night that cellphones and other handheld communication devices continue to be banned near sensitive equipment there, including ventilators and incubators.

While a few hospitals have begun to buck the trend, conventional wisdom supports the VCH's view that these devices could interfere with crucial equipment.

Typical of this concern were warnings from the U.S. Federal Communications Commission that electromagnetic waves from cellphones could shut down electronic devices in hospitals.

These fears were firmly enough entrenched to have made their way into popular legend.

According to an e-mail that made the rounds in 2003, a young girl died during a routine operation because "some idiot" used a cellphone near the operating theatre.

"Be compassionate," this e-mail went on to urge. "Do not use your hand phone at any hospital or places where you are told not to use it. You might not be caught in the act, but you might have killed someone without knowing it."

That message was later debunked by snopes.com (an Internet site about urban legends), and, according to a study released by the Mayo Clinic, the fears it addresses are groundless.

The article goes on to note some of the findings of the Mayo Clinic study then returns to a comment from the Vancouver Hospital.

But the policy-makers at VCH are not convinced. Spokeswoman Brandy Delves said the hospital has had the same policy since 1996, banning cellphones and other hand-held communication devices in key areas. "We have reviewed all the recent literature and have decided to keep our current policy," she said last night.

This is interesting. It's very hard to prove a negative so one can't expect absolute "proof" that cellphones are harmless in a hospital setting. Once the idea of possible danger has been planted it always seems better to be safe than sorry. Nevertheless, all of the so-called evidence of danger has been refuted and there are hospitals that have lifted the ban. Those hospitals do not seem to be losing patients due to unexpected equipment failures. In light of data like this why would "policy-makers," many of whom are doctors, not make a rational decision to lift the ban?

What is it about our psychology that causes some people to reject scientific/rational evidence when it conflicts with their superstitions? Even people who are trained in "evidence-based" medicine seem to be incapable of applying the methodology in real life.

The Molecular Basis of Roundup® Resistance

Recall that glyphosate inhibits the enzyme EPSP synthase, an enzyme that catalyzes the following reaction in the chorsimate biosynthesis pathway [How Roundup® Works].

Funke et al. (2006) explored the molecular basis of this inhibition by looking at the structure of EPSP synthase from the C4 strain of Agrobacterium sp. This is the resistant form of the enzyme that has been genetically engineered into Roundup Ready® plants [Roundup Ready® Transgenic Plants].

Note that the structure of glyphosate resembles one of the substrates of the reaction; namely phosphoenolpyruvate (PEP). It was already known that glyphosate binds tightly to the active site of the enzyme and inhibits the reaction by preventing PEP binding. As it turns out, the site for glyphosate binding is exactly the same as the site for PEP binding and this explains the inhibition.

Funke et al. (2006) looked at the C4 EPSP enzyme with and without one of the other substrates: namely, shikimate-3-phosphate (sometimes called shikimate-5-phosphate). The results reveal the precise location of the active site of the enzyme at the base of a cleft between two domains. This form of the enzyme is called class II EPSP synthase because it is distantly related to the class I enzymes in other bacteria and eukaryotes (30% amino acid sequence identity). This is the first paper to examine the structure of a class II enzyme.

As an aside, notice that the enzyme closes up a little bit when the substrate binds—sort of like a Pacman icon. This mechanism of substrate binding is called induced fit and it's proving to be more common than most people realized.

The glyphosate resistant (Roundup Ready®) mutation in C4 EPSP synthase is a substitution of Alanine (A) for Glycine (G) at amino acid position 100. The glyphosate molecule fits nicely into the wild type G100 form of the enzyme (lower image) and it excludes PEP binding completely. Note that glyphosate (green) is in an extended configuration when it is bound. The dotted lines represent non-covalent interactions between the enzyme and the glyphosate molecule. The blue dots are "frozen" water molecules embedded in the active site.

In the mutant form of the enzyme the extra methyl group on alanine is just big enough to cause glyphosate to distort so it can no longer lie in the optimal extended configuration (top image). This means that glyphosate binds much more weakly and doesn't inhibit enzyme activity.

The important point is that the active site can still accommodate phosphoenolpyruvate because it is smaller than glyphosate. What this means is that the overall activity of the enzyme in the absence of glyphosate is unaffected. There are lots of EPSP synthase mutants that don't bind glyphosate but in almost all cases the rate of the reaction is drastically reduced because PEP binding is also weakened. For example, if you mutate the glycine to alanine at the equivalent position in other bacterial or plant enzymes you abolish PEP binding along with glyphosate binding.

What's special about the class II enzymes in general and the Agrobacterium sp. enzyme in particular, is that the amino acids surrounding the PEP binding pocket are positioned just right so that a slight shift can exclude glyphosate without affecting phosphoenolpyruvate. This is mostly due to the positions of the charged amino acid side chains that form weak interactions with the oxygen atoms and the nitrogen of glyphosate; for example, arginines (R) at 128, 357, and 405; lysine (K) at 28; and glutamate (E) at 354.

The results of this study not only shed light on the mechanism of glyphosate resistance but they also help explain the lack of Roundup® resistant plants. Apparently, the class I enzymes in plants have a binding pocket that is difficult to mutate in a way that excludes glyphosate while still allowing PEP binding. Nevertheless, some examples of Roundup® resistant plants are known. I'll describe them tomorrow.

(Funke et al. had to do a bit of sleuthing and reconstruction in order to solve the structure of the C4 EPSP synthase. The C4 strain of Agrobacterium sp. has, naturally enough, not been given out to scientists outside of Monsanto laboratories. So Funke et al. got the amino acid sequence from US Patent 5633435 and reverse engineered the nucleotide sequence of the gene. They synthesized the nucleotide sequence and amplified the fragments by PCR. They then tacked on a promoter and a transcription termination signal and cloned the articfial gene into an E. coli plasmid. The artificially reconstructed protein was then expressed in E. coli, isolated, purified, and crystallized.)

Funke, T., Han, H., Healy-Fried, M,L., Fischer, M., and Schonbrunn, E. (2006) Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. (USA) 103:13010-13015. [PubMed]

Jim Watson Comments on GM Crops and Recombinant DNA Technology

 
Watch this clip of Jim Watson commenting on recombinant DNA technology and its uses in making genetically modified plants [Dr. James Watso]. The video is produced by Monsanto so those of you with a bias can easily dismiss it without a second thought.

The rest of you should pause to think about what Watson is saying. He's definitely outspoken but is he right? He says ...

Recombinant DNA is the safest technology I’ve ever heard.

Read Nobel Laureate: Paul Berg for information about Asilomar and the recombinant DNA controversy of the 1970's. Read the comments to that article for other points of view and references to Watson. Hsien Hsien Lei has an opinion and so does Jeremy.

The Great Muffin Joke Debate

 
Check out The Great Muffin Joke Debate at Cosmic Variance. I think it's funny. It's not ROTFLMFHO funny, but it does make me smile. John Tierney does not think it's funny. Is there a correlation between whether you think the joke is funny and whether you "get" irony and sarcasm?

A New Understanding of the Early Evolution of Flowering Plants

 
The folks over at the UBC Botanical Gardens have written an easy-to-understand summary of the recently published Nature paper on Hydatellaceae [A New Understanding of the Early Evolution of Flowering Plants].

Turns out that Hydatellaceae, a family of flowering plants, diverged from other flowering plants before the monocot-dicot split. They are related to water lilies, another group that branches deep in the tree of flowering plants. There are some pretty pictures of various species in the Hydatellaceae family over on the Botany Photo of the Day website. The one shown here is Trithuria submersa a species from Western Australia. These are very small plants and most of them are only found in Australia and New Zealand.

Proof That God Exists from a Prestigious Journal

 
EukekAlert! reports proof that God exists [Does God answer prayer? ASU research says 'yes'].

The answer, according to a new Arizona State University study published in the March journal Research on Social Work Practice, is “yes.” David R. Hodge, an assistant professor of social work in the College of Human Services at Arizona State University, conducted a comprehensive analysis of 17 major studies on the effects of intercessory prayer – or prayer that is offered for the benefit of another person – among people with psychological or medical problems. He found a positive effect.

“There have been a number of studies on intercessory prayer, or prayer offered for the benefit of another person,” said Hodge, a leading expert on spirituality and religion. “Some have found positive results for prayer. Others have found no effect. Conducting a meta-analysis takes into account the entire body of empirical research on intercessory prayer. Using this procedure, we find that prayer offered on behalf of another yields positive results.”

Hodge’s work is featured in the March, 2007, issue of Research on Social Work Practice, a disciplinary journal devoted to the publication of empirical research on practice outcomes. It is widely recognized as one of the most prestigious journals in the field of social work.

Hmmmm ... "one of the most prestigious journal in the field of social work." Well, that does it for me. Where's the nearest church? Pray for me.

Roundup Ready® Transgenic Plants

By the late 1990's it was apparent that recombinant DNA technology [see Nobel Laureate: Paul Berg] had advanced to the point where it was feasible to consider the production of genetically modified crops. One of the first targets was the creation of plants that were resistant to the herbicide glyphosate or Roundup® [How Roundup® Works].

Surprisingly, in spite of extensive spraying with Roundup® no resistant plant species had been detected. Since the target of glyphosate, EPSP synthase (EC 2.5.1.19), is also present in bacteria, a search for resistant bacteria was undertaken. The idea is that if a glyphosate-resistant enzyme from bacteria could be transferred to plants it might make the plants resistant to the herbicide. Such Roundup Ready® transgenic plants be an enormous advantage for farmers since a crop of, say Roundup Ready® soybean, could be sprayed with Roundup® to kill all weeds without affecting the crop.

Coincidently , it would be of enormous advantage to Monsanto, the manufacturer of Roundup®, especially if they could control the distribution of the genetically modified plants.

The C4 strain of Agrobacterium sp. proved to be just the thing. This is a species of bacteria that was found growing in the waste-fed column at a factory that made glyphosate. The EPSP synthase enzyme from this bacterium (C4 EPSP synthase) was almost completely insensitive to glyphosate.

The C4 EPSP bacterial gene was cloned and inserted into a bacterial plant vector in order to prepare for cloning into plants. The details of one of the Monsanto C4 EPSP cloning vectors are shown in the first patent filed on September 13, 1994 [US Patent 05633435].

This is a modifed bacterial plasmid vector designed to be propagated in E. coli (for cloning and construction) and Agrobacterium tumefaciens (for transforming plants). Ori-322 is an origin of replication from plasmid pBr322. It is used in E. coli to replicate the plasmid. Ori-V is an origin from plasmid RK2, a plasmid that can propagate in a wide variety of gram negative bacteria, including Agrobacterium tumefaciens. Rop is a small gene that encodes a protein requried to maintain plasmid copy number in bacteria.

There are two selectable markers. SPC/STR encodes a protein conferring spectinomycin/streptomycin resistance. The gene is derived from transposon Tn7. AAC(3)-III encodes bacterial gentamycin-3-N-acetyl transferase type III allowing selection for gentamycin resistance in plants. The bacterial AAC(3)-III gene has to be modified in order to allow effient expression in plant cells. A plant promoter (P-35S) is inserted at the 5' end. This promoter is the 35S promoter from cauliflower mosaic virus (CaMV). The 3' end of the gene is modified by inserting the polyadenylation site (NOS 3') from the nopaline synthase gene of the tumor-inducing (Ti) plasmid from Agrobacterium tumefaciens.

Similarly, the bacterial C4 EPSP gene was modified to have a strong plant promoter (P-e35S, related to P-35S) and a polyadenylation site (NOS 3'). One additional modification is necessary because the plant EPSP synthase is in chloroplasts where synthesis of chorimsate takes place. The bacterial gene has to have an N-terminal leader sequence that targets the protein to the chloroplast. This is supplied by CTP2, the chloroplast transit peptide from the Arabidopsis (wall cress) EPSP synthase gene.

The shuttle plasmid is built in E. coli then purified plasmid DNA is used to transform Agrobacterium tumefaciens. This bacterium infects plants and injects DNA from a Ti-like plasmid into plant cells where it enters the nucleus and becomes incorporated into the plant chromsomes. Under normal circumstances Agrobacterium tumefaciens causes gall tumors in plants but in this case the recombinat DNA is transferred and no tumors are formed. The transformation is mediated by cutting the plasmid at the RIGHT BORDER to produce a linear DNA molecule. Defective Ti plasmids in the bacterial cell are required to promote the transfer of the recombinant DNA.

The interesting feature of this transformation is that it is mediated by the bacteria. All you need to do is expose the plant cells to the bacteria under the right conditions and your gene of interest will end up in a plant chromsome.

The complete process begins with the isolation of small bits of plant tissue. They are grown on nutrient plates before being exposed to the bacteria carying the recombinant DNA plasmid.

Transformed cells will start to grow and they can eventually be isolated and transferred to a liquid that promotes shoot growth. After a few weeks you end up with an entire plant carrying the recombinant DNA. This plant is then propagated to produce thousands of genetically modified plants and seeds.

Roundup Ready® soybean was the first crop plant produced by Monsanto. Today, 90% of the soybean crop in the USA consists of Roundup Ready® plants. You can't buy soybean products that don't come from genetically modified plants.

Two thirds of the cotton and a quarter of the corn crop are Roundup Ready® plants. There is some resistance to growing Roundup Ready® wheat.

Nobel Laureate: Paul Berg

 
The Nobel Prize in Chemistry 1980.

"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"


Paul Berg won the Nobel Prize in 1980 for his work on developing recombinant DNA technology. This is the only Nobel Prize that has been awarded for that achievement.

Berg is credited with creating the first recombinant DNA molecule back in 1972 (Jackson et al. 1972). He combined a fragment of a bacterial plasmid with a piece of DNA from a simian virus (SV40). The goal was to understand the structure and organization of the small SV40 virus—the main focus of research in Berg's laboratory. Berg was hoping to create a recombinant DNA vector that would introduce foreign DNA into mammalian cells where it could be expressed. Here's part of the original press release ...

Berg was the first investigator to construct a recombinant-DNA molecule, i.e. a molecule containing parts of DNA from different species, e.g. a chromosome from a virus combined which genes from a bacterial chromosome. His pioneering experiment has resulted in the development of a new technology, often called genetic engineering or gene manipulation, which has already had important practical applications, e.g. the manufacture of human hormone with the aid of bacteria. Berg performed his experiment, however, as part of an incisive analysis of the chromosome of an ape virus (called SV 40) Viruses contain DNA (or sometimes RNA, another nucleic acid). They cause disease by introducing foreign genetic information in a cell and in this way disturbing its chemical machinery. As DNA molecules from viruses are relatively small, they are excellent objects of investigation for the study of the relationship between the chemical structure and biological function of DNA.

Following the creation of the first recombinant DNA molecule—but after a lag of a few years—Paul Berg was successful in his attempt to construct mammalian cloning vectors. His lab was the first to express a cloned foreign gene in mammalian cells. In this case it was the recently cloned rabbit β-globin gene.

The original recombinant DNA molecule constructed in 1972 was not immediately propagated in living cells out of safety concerns. At the time, it was unclear whether the cloning of a potential cancer causing virus (SV40) presented a health hazard. Berg and others voluntarily stopped research in this field until they could sort out the safety issues.

The voluntary moratorium in 1973-74 led to the famous Asilomar Conference where the issue was debated by a group of prominent scientists. This was such an important event that a 2004 article by Paul Berg on the Asilomar Conference is included in the Nobel Prize website [Asilomar and Recombinant DNA]. The result of the debate was a decision to proceed with caution and a number of safety protocols for working with recombinant DNA were put in place.

Almost all of the safety concerns proved to be exaggerated and the recombinant DNA regulations have been quietly dropped over the years. Even in 1980, when Berg received his Nobel Prize, he was able to express some frustration at how the concerns of scientiests were perceived. Nevertheless, there's a common perception among scientists that their behavior in the mid-1970's was not only ethical but highly successful. That point of view is expressed in the 2004 article ...

What did the actions taken by the scientific community achieve? First and foremost, we gained the public's trust, for it was the very scientists who were most involved in the work and had every incentive to be left free to pursue their dream that called attention to the risks inherent in the experiments they were doing. Aside from unprecedented nature of that action, the scientists' call for a temporary halt to the experiments that most concerned them and the assumption of responsibility for assessing and dealing with those risks was widely acclaimed as laudable ethical behavior. If the Asilomar exercise was a success, it was because scientists took the initiative in raising the issue rather than having it raised against them; that initiative engendered considerable credibility instead of cynical suspicion of what was to follow. The public's trust was undeniably increased by the fact that more than 10% of the participants were from the news media. They were free to describe, comment on and criticize the discussions and conclusions at the end of the conference. All the deliberations, bickering, bitter accusations, wavering views and the arrival at a consensus were widely chronicled by the reporters that attended and subsequently by the rest of the media and subsequent commentators.

While much of that may be true, it tends to ignore the consequences that we had to live with for a decade. By 1980 it was clear that recombinant DNA posed no danger but by then all the strict rules and regulations were in place and compliance was enforced by law. At that point the opinions of the experts didn't matter. The public was scared and they were determined to ignore scientific evidence in order to restrict research. We've also forgotten the serious attempts by uninformed governments to stop recombinant DNA research altogether.

The cynical point of view is that the public's trust in science declined in the 1970's because scientists were pushing ahead with highly dangerous research that could destroy the world.

So, what are the lessons of Asilomar? Here's how Berg describes it in 2004 ..

Is "the Asilomar model" appropriate for resolving or contributing to some of the "hot button" issues confronting scientists and the public today? For example, are the deep divisions about fetal tissue and embryonic stem cell research, somatic and germ-line gene therapy and directed genetic modification of food crops amenable to deliberation and resolution? I believe the Asilomar model would not succeed in dealing with those issues today to the extent it did 30 years ago with recombinant DNA for the following reasons. First, the public's awareness of the recombinant DNA breakthrough was sudden and unanticipated. It was more than just another interesting scientific advance because it brought with it potential dangers to public health. Furthermore, the implications of risk came from the scientists conducting that research, not from some investigative reporter or disaffected scientist; that was most unusual, even historic. There seemed to be an urgent need for consensus on how to proceed and a plausible plan on how to deal with issues, both of which were provided by the scientific community. Action was prompt and seen by the public to have been achieved by transparent deliberations and with considerable cost to their own scientific interests. The issue and its resolution were complete before an entrenched, intransigent and chronic opposition developed. Attempts to prohibit the research or reverse the actions recommended by the conference threatened but never generated sufficient traction to succeed.

By contrast, the issues that challenge us today are qualitatively different. They are often beset with economic self-interest and increasingly by nearly irreconcilable ethical and religious conflicts and challenges to deeply held social values. An Asilomar type conference trying to contend with such contentious views is, I believe, doomed to acrimony and policy stagnation, neither of which advances the cause of finding a solution. There are many forums for airing opposing views but emerging with an agreed upon solution from such an exercise is elusive and discouraging.

The Asilomar decisions emerged from a consensus of opposing views. Although the recommendations were clearly "inconvenient", the participants had a stake in having the science move forward and not in leaving the rules for conducting the research to be set by others. By contrast, there is little prospect for consensus in our society on the ethical issues concerning fetal tissue and embryonic stem cell research, genetic testing, somatic and germ-line gene therapy, and engineered plant and animal species and hence little incentive to seek a compromise. Compromise in those instances may only be achievable by political means, where majority rule prevails.

In other words, the lesson of Asilomar is that when politicians and the general public learn enough about an issue to start forming an opinion, the views of scientists are usually ignored or rejected. It's better to keep them ignorant until you can get some reasonable laws passed. Not a very happy lesson.

Jackson, D.A., Symons, R.H., and Berg, P. (1972) Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. (USA) 69:2904-2909 [PubMed]

Please Tell Me This Is a Joke

 
From Biology News Net comes this crazy article [Why aren't humans furry? Stone-Age moms could be the answer.

Medical Hypotheses, an Elsevier publication, has announced the winner of the 2006 David Horrobin Prize for medical theory. Written by Judith Rich-Harris, author of The Nurture Assumption and No Two Alike, the article, "Parental selection: a third selection process in the evolution of human hairlessness and skin color" was judged to best embody the spirit of the journal. The £1,000 prize, launched in 2004, is awarded annually and named in honour of Dr. David Horrobin, the renowned researcher, biotechnology expert and founder of Medical Hypotheses who died in 2003.

Harris' paper describes Stone Age societies in which the mother of a newborn had to decide whether she had the resources to nurture her baby. The newborn's appearance probably influenced whether the mother kept or abandoned it. An attractive baby was more likely to be kept and reared.

Harris' theory is that this kind of parental selection may have been an important force in evolution. If Stone Age people believed that hairless babies were more attractive than hairy ones, this could explain why humans are the only apes lacking a coat of fur. Harris suggests that Neanderthals must have been furry in order to survive the Ice Age. Our species would have seen them as "animals" and potential prey. Harris’ hypothesis continues that Neanderthals went extinct because human ancestors ate them.

This year's prize judge was Professor Jonathan Rees FMedSci of Edinburgh University, Scotland – co-discoverer of the 'red hair gene'. Professor Rees said: "This paper is an excellent example of the kind of bold thinking and theorizing which David Horrobin intended to encourage when he began Medical Hypotheses. I hope that Judith Rich Harris' idea provokes debate and further investigation of this topic."

This can't be correct, can it? An apparently respectable organization giving a prize to someone who postulates that stone-age women killed off their hairy children and kept the hairless ones and that's why we don't have hair? It's a joke, right?

"Bold thinking" indeed. I can think of better words to describe that "theory."

Genome Size in Birds

 
The Animal Genome Size Database is maintained by T. Ryan Gregory of the University of Guelph in Ontario. Gregory has collected data on genome size in animals from the scientific literature and from work in his own lab. He is interested in several projects on genome evolution.

There are several ways of reporting genome size. The most common is to give the C-value (haploid genome size) in picograms (pg) because a lot of the data simply measures the amount of DNA in a nucleus using a DNA-specific stain. The range of C-values for different groups of organisms is shown in the figure (above right). As the legend states, there's no special significance to the order of the groups (from top to bottom) other than the fact that it's easy to understand if mammals are at the top.

One of the things that Gregory works on is the correlation between cell size and genome size. It turns out that the size of the nucleus is related to the size of the cell, such that large genomes give rise to large nuclei and large cells. This is particularly evident when you look at red blood cells and Gregory has a remarkable image showing this correlation on his website [Gregory Lab].

It has been known for some time that birds have smaller genomes than reptiles and mammals. This has natually given rise to an adaptionist explanation;namely, that the small genome is due to selection for small cells in birds because they exert a lot of energy in flight. In other words, small genomes are an adaption for flight.

A recent News article on the Nature website raises an important question concerning this adaptionist explanation. If birds have smaller genomes than other vertebrates then is that a derived trait or did birds inherit a small genome from their dinosaur ancestors? [Did a 'light' genome help birds take flight?].

A study of dinosaur genomes hints that the early evolution of a smaller genome might have been necessary for later vertebrates to take to the skies.

Birds have long been known to have much smaller genomes than mammals and reptiles living on the ground. And a small genome has been linked to both small cell size and high metabolic rate: the lower volume-to-surface ratio of small cells, which don't have much DNA to pack inside, can allow for faster transport of nutrients and signals across the membrane. Thus, some suggest that the energetic demands of flight require birds to have a 'light' genome.

But which came first: flying birds or the smaller genome?

The paper by Organ et al. (2007) looked at genome size in extinct dinosaurs with a view to discovering whether the bird ancestors had large or small genomes. Obviously, they couldn't measure genome size directly in fossils. What they did was measure the size of fossilized cells, having previously established that there's a correlation between the size of cells and the size of the nucleus. The size of the nucleus, in turn, depends on the amount of DNA in the genome.

The result is shown below. Red and purple lines indicate species with small genomes. You can see that the bird lineages (Aves) all have smallish genomes. So do the theropods that cluster with the birds on the right-hand group within Dinosauria. What this means is that the entire group of dinosaurs that descended from theropods had small genomes. It means that birds, which didn't arise until later, inherited their small genomes from ancestral theropods.

The result indicates that small genome size in birds is not an adaptation for flight. Perhaps it is not an adaptation at all but simply an accident due to the fact that the ancestor of sauropods just happened to have a reduced genome.

Before I had a chance to prepare this article, Carl Zimmer had not only done the work and interviewed Gregory, but he had published the review on the Science website [Jurassic Genome]!!! Please read Zimmer's excellent article for a more complete story.

Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M., and Edwards, S.V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180-184. [PubMed]