Changing Your Mind: Alan Alda Converts from Atheism to Agnosticism

 
Alan Alda has changed his mind. He used to be an atheist but now he prefers to call himself an agnostic [ So far, I've changed my mind twice about God].

But, slowly I realized that in the popular mind the word atheist was coming to mean something more: a statement that there couldn't be a God. God was, in this formulation, not possible, and this was something that could be proved. But I had been changed by eleven years of interviewing six or seven hundred scientists around the world on the television program Scientific American Frontiers. And that change was reflected in how I would now identify myself.

The most striking thing about the scientists I met was their complete dedication to evidence. It reminded me of the wonderfully plainspoken words of Richard Feynman who felt it was better not to know than to know something that was wrong. The problem for me was that just as I couldn't find any evidence that there was a god, I couldn't find any that there wasn't a god. I would have to call myself an agnostic. At first, this seemed a little wimpy, but after a while I began to hope it might be an example of Feynman's heroic willingness to accept, even glory in, uncertainty.

I think he's dead wrong about the meaning of the word atheism. I think it means that you have not accepted theism and therefore you are "without a belief in God." I see the word atheism as similar to words like "a-toothfairyism" or "a-SantaClausism." You don't believe in Santa Claus so you are an "a-SantaClausist." It does not mean you are committed to the concept that there could not possibly be a Santa Claus.

It would be silly to label yourself an agnostic with respect to belief in Santa Claus. Nobody, especially Christians, goes around announcing that they are agnostic about the existence of the Greek Gods. You don't believe in them, full stop.

There is a version of agnosticism that's perfectly acceptable. John Wilkins, among others, promotes this definition of agnosticism. True agnostics claim that it is impossible to prove one way or the other whether God exists, just as it's impossible to prove one way or the other whether the tooth fairly exists. All rational people are agnostics in this sense. Some of them are also atheists. Alan Alda appears to be both an atheist and an agnostic, just like Richard Dawkins. Alan Alda is a wimp for letting non-atheists redefine atheism and then abandoning his position because of that incorrect definition.

It's not an either/or situation, in my opinion (Wilkins disagrees). You can, and should, be both an atheist and an agnostic.

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[Photo Credit: M*A*S*H]

Changing Your Mind: The Limits Of Darwinian Reasoning

 
Marc D. Hauser is a biologist and psychologist at Harvard University (USA). He is beginning to see the error of his adaptationist ways [The Limits Of Darwinian Reasoning].

Let me be clear about the claim here. I am not rejecting Darwin’s emphasis on comparative approaches, that is, the use of phylogenetic or historical data. I still practice this approach, contrasting the abilities of humans and animals in the service of understanding what is uniquely human and what is shared. And I still think our cognitive prowess evolved, and that the human brain and mind can be studied in some of the same ways that we study other bits of anatomy and behavior. But where I have lost the faith, so to speak, is in the power of the adaptive program to explain or predict particular design features of human thought.

Although it is certainly reasonable to say that language, morality and music have design features that are adaptive, that would enhance reproduction and survival, evidence for such claims is sorely missing. Further, for those who wish to argue that the evidence comes from the complexity of the behavior itself, and the absurdly low odds of constructing such complexity by chance, these arguments just don’t cut it with respect to explaining or predicting the intricacies of language, morality, music or many other domains of knowledge.

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Changing Your Mind: The Obligations and Responsibilities of The Scientist

 
Leon Lederman is a physicist and a Nobel Laureate. He has changed his mind about the The Obligations and Responsibilities of The Scientist.

The role of the Professor, reflecting the mission of the University, is research and dissemination of the knowledge gained. However, the Professor has many citizenship obligations: to his community, State and Nation, to his University, to his field of research, e.g. physics, to his students. In the latter case, one must add to the content knowledge transferred, the moral and ethical concerns that science brings to society. So scientists have an obligation to communicate their knowledge, popularize, and whenever relevant, bring his knowledge to bear on the issues of the time. However, additionally, scientists play a large role in advisory boards and systems from the President's Advisory system all the way to local school boards and PTAs. I have always believed that the above menu more or less covered all the obligations and responsibilities of the scientist. His most sacred obligation is to continue to do science. Now I know that I was dead wrong.

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Changing Your Mind: Maybe Human Races Do Exist After All

 
Mark Pagel is an evolutionary biologist who used to buy into the idea that human races did not exist [We Differ More Than We Thought].

The last thirty to forty years of social science has brought an overbearing censorship to the way we are allowed to think and talk about the diversity of people on Earth. People of Siberian descent, New Guinean Highlanders, those from the Indian sub-continent, Caucasians, Australian aborigines, Polynesians, Africans — we are, officially, all the same: there are no races.

Now, in 2007, he changed his mind ...

What this all means is that, like it or not, there may be many genetic differences among human populations — including differences that may even correspond to old categories of 'race' — that are real differences in the sense of making one group better than another at responding to some particular environmental problem. This in no way says one group is in general 'superior' to another, or that one group should be preferred over another. But it warns us that we must be prepared to discuss genetic differences among human populations.

Good for him. Better late than never, I say.

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Changing Your Mind: The Fallacy of Hypothesis Testing

 
The Edge has asked people to describe whether they have changed their mind about anything and if so, why? It's the Annual Question for 2008.

Some of the replies are worth discussing. For example, Irene Pepperbreg has changed her mind about the meaning of the scientific method [The Fallacy of Hypothesis Testing]. I think she makes some good points, notably ....

Third, I've learned that the scientific community's emphasis on hypothesis-based research leads too many scientists to devise experiments to prove, rather than test, their hypotheses. Many journal submissions lack any discussion of alternative competing hypotheses: Researchers don't seem to realize that collecting data that are consistent with their original hypothesis doesn't mean that it is unconditionally true. Alternatively, they buy into the fallacy that absence of evidence for something is always evidence of its absence.

I'm all for rigor in scientific research — but let's emphasize the gathering of knowledge rather than the proving of a point.

I think this is a serious problem in science today. There are too many papers being published without any serious discussion of competing explanations. There are too many papers that fail to critically examine their own basic assumptions or the possible flaws in their experiments.

There may be a reason for this behavior—scientists don't want to draw attention to possible flaws in their work for fear that the granting agency will find out—but that doesn't excuse it. Scientific rigor demands that you present both sides of a scientific debate in a fair and unbiased manner. The failure to address the arguments of your opponents is nothing less than failing to be a good scientist.

Similarly, the failure to recognize the possible flaws in one's own explanation is the mark of a bad scientist.

While Irene Pepperbreg may be right about the flaws in today's method of doing science, I'm not prepared to throw out the baby with the bathwater. Hypothesis-based science is still important. You just have to form the right hypotheses and put your work in context. The problem, in my opinion, isn't that hypothesis testing is a fallacy: the problem is that it's not being done properly.

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Open Lab 2007

 
Open Lab 2007 is about to be published. The book contains the best articles from science blogs in 2007.

There were 486 articles nominated and the judges selected 53 for publication [Open Lab 2007 - the winning entries for you to see!]. The winners come from a wide selection of science blogs; 20 of them are part of the SEED group (ScienceBlogs^TM) and 33 are from other science blogs.

For the second year in a row there won't be any of my Sandwalk postings in the Open Lab anthology.

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Oops! The Rapture Didn't Happen

 
There was supposed to be a rapture last month but the prediction didn't come true. Either that or it did come true and only a small number of people were raptured, not including the prophet.

In case anyone is interested, here's how our prophet explains his little mistake [Are You Rapture Ready]. I assume he's apologizing to all those people who gave away everything in the expectation that they would soon be in heaven.

I offered to take some of those worldly goods off their hands but I couldn't find anyone who was expecting to be raptured. I guess I don't hang out with the right kinds of people.

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Iowa Caucuses

 
In a few days about 100,000 people will get together in Iowa to elect the next President of the United States. At least I think that's what the caucuses are all about. It's all very confusing. Apparently there are some other states like New Hampshire and South Carolina that have to confirm the Iowa result before it becomes official.

American politics is so confusing. None of this stuff is in the Constitution so I can't check the rules.

Anyway, since those few Iowa citizens are going to have such an important role in choosing the new leader of the free world (sic) I thought you might be interested in seeing how one of them is struggling to make up his mind. John Logsdon of Sex, genes & evolution has written about his quandary [Caucus Conundrum: Considering Compelling Candidates]. Why not pay him a visit and help him decide?

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You Think *You* Have a Tough Job? ....

 

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[Hat Tip: Canadian Cynic]

Airport Security and Liquid Contraband

 
The other day I saw a photograph of an airport security guard standing in front of dozens of large plastic bags full of confiscated liquids. The bags were stacked in a corridor and passengers were streaming by.

"Isn't this strange," I thought. Those bags are full of potentially dangerous chemicals that could destroy an aircraft yet the security guard seems unconcerned about the potential threat. As it turns out, there are lots of people who think that airport security is a farce. Patrick Smith has written about it in today's New York Times [The Airport Security Follies].

“I would not hesitate to allow that liquid explosives can pose a danger,” Greene added, recalling Ramzi Yousef’s 1994 detonation of a small nitroglycerine bomb aboard Philippine Airlines Flight 434. The explosion was a test run for the so-called “Project Bojinka,” an Al Qaeda scheme to simultaneously destroy a dozen widebody airliners over the Pacific Ocean. “But the idea that confiscating someone’s toothpaste is going to keep us safe is too ridiculous to entertain.”

Yet that’s exactly what we’ve been doing. The three-ounce container rule is silly enough — after all, what’s to stop somebody from carrying several small bottles each full of the same substance — but consider for a moment the hypocrisy of T.S.A.’s confiscation policy. At every concourse checkpoint you’ll see a bin or barrel brimming with contraband containers taken from passengers for having exceeded the volume limit. Now, the assumption has to be that the materials in those containers are potentially hazardous. If not, why were they seized in the first place? But if so, why are they dumped unceremoniously into the trash? They are not quarantined or handed over to the bomb squad; they are simply thrown away. The agency seems to be saying that it knows these things are harmless. But it’s going to steal them anyway, and either you accept it or you don’t fly.

It's about time that we started to protest against the waste of time and effort at airport security lines. This is a huge over-reaction to 9/11 and the fear of terrorism.

Read what John Wilkins has to say on Evolving Thoughts [Follies d'Air]. He puts things into historical perspective and points out that we are not only being inconvenienced by such folly but also surrendering considerable rights and freedoms in the name of "security." You'll appreciate John's ability to link airport security measures with Julius Caesar and the Prussians.

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[Photo Credit: Tim Boyle/Getty Images from the MSNBC website (Where will all that liquid contraband go?)]

Atheists Are Intolerant and Militant

 
Here's a video from "TheismBeatsAtheism." It's quite well done but still reflects the hollowness of the typical theist. Note that there's a lot of complaining about the "intolerance" and "militancy" of the atheists but very little defense of theism. The best proof they can offer for God's existence is the fact that 80-90% of American believe in him.

The theists are going to have to do better than this. If there is evidence of a supernatural being then let's hear it. I'm sick of those theists who claim that we have to read some "sophisticated" Christian apologetics in order to understand the arguments for God's existence. Those arguments have been around for 2000 years or more and none of them stand up to rational examination. (Note that they never recommend any Hindu books. Why is that? Every religion has their share of "sophisticated" books proving that their particular religion is correct. What does that tell you?)

I like the part where they complain about the universities. Apparently, getting a college education and learning how to think is detrimental to one's belief in a supernatural being. Do they have solutions to this problem, other than promoting ignorance? Yes, they do—more effort on brainwashing young children ought to work. What's interesting is that these theist dudes would complain about brainwashing by other religions¹ but see nothing wrong with Christians doing it.

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1. Especially the Muslim bogeyman. You might be surprised to learn than all Muslims are intolerant and would kill any atheist who lectured to them. I guess it's okay for Christians to be militant and intolerant toward other religions but not okay for atheists. I loathe hypocrisy.

[Hat Tip: Hemant Mehta at Friendly Atheist (These Atheists… They’re Everywhere!)]

DNA Denaturation and Renaturation and the Role of Hydrogen Bonds and Stacking Interactions

 
Several students have written to me with questions about the structure of DNA. The most troubling questions are from students who have read the article I wrote about a paper that measures the stacking interactions in polynucleotides [Measuring Stacking Interactions]. In that posting I wrote ...

The two strands of double- stranded DNA are held together by a number of weak interactions such as hydrogen bonds, stacking interactions, and hydrophobic effects [The Three-Dimensional Structure of DNA].

Of these, the stacking interactions between base pairs are the most significant. The strength of base stacking interactions depends on the bases. It is strongest for stacks of G/C base pairs and weakest for stacks of A/T base pairs and that's why it's easier to melt A/T rich DNA at high temperature. (It is often incorrectly assumed that this is due to having only two hydrogen bonds between A/T base pairs and three between G/C base pairs.)

THEME

Deoxyribonucleic Acid (DNA)Many students have written to say that my statements contradict their Professors and their textbooks. I'm not surprised. The old-fashioned view of DNA denaturation (pre-1990) supposed that the differences between A/T rich DNA and G/C rich DNA were due to the extra hydrogen bond in G/C base pairs. Many of the Professors who teach introductory biochemistry aren't aware of the fact that this view is incorrect. Even more surprising, some of the current textbooks have not bothered to update their material on the structure of DNA.

Here's the story as we know it today. For those students who have written to me, I repeat the caution I mentioned in my reply to you—be sure to check with your Professor before you write any tests. Make sure he/she understands why you are contradicting what was said in class so you don't get marks taken off. It's always better to do this in advance instead of arguing your case after you have lost marks on the test.

Let's look first at what happens when DNA is denatured by raising the temperature.

As the temperature increases, you start to get local unwinding of the double-stranded DNA. This unwinding occurs preferentially in regions where the two strand are held together less strongly. In these regions the strands separate to form bubbles of single-stranded regions. The DNA sequence in these regions is enriched in A/T base pairs because the interactions between the two strands are weaker in A/T rich regions. In G/C rich regions strands are held together more strongly so they don't unwind until higher temperatures.

Incidentally, even at normal cell temperatures the DNA "breathes" and local regions become temporarily unwound. As you might expect, A/T rich regions are more likely to open up than G/C rich regions. This is one of the reasons why transcription initiation bubbles and DNA replication origins are often A/T rich. It's easier for the proteins (RNA polymerase, and origin binding proteins) to create the locally unwound regions.

When all of the base interactions are broken, the two strands separate. This is called denaturation. (Local unwinding is not denaturation.)

The base are now exposed to the aqueous environment. Single-stranded DNA is more stable than double-stranded DNA at higher temperature. Note that the edges of the bases will still form hydrogen bonds in this situation. They form hydrogen bonds with water molecules. In fact, they will form many more hydrogen bonds with water than they would form with complementary bases in double-stranded DNA.

As the temperature is lowered, the double-stranded form becomes more stable than the single strand in solution, and the DNA renatures. The first step is a nucleation event where two complementary regions come into contact. Nucleation is the rate-limiting step in renaturation. Once nucleation occurs, the rest of the molecule zips up pretty quickly.

It's easy to follow the denaturation of DNA because there's a difference in the absorbance of ultraviolet light between single- and double-stranded DNA. Single-stranded DNA absorbs more strongly.

In a typical melting curve, you measure the increase in UV absorbance as the temperature increases. This tracks the unwinding and denaturation of DNA. The melting point (T_m) is the temperature at which half the DNA is unwound.

DNA that consists entirely of AT base pairs melts at about 70° and DNA that has only G/C base pairs melts at over 100°. You can calculate the T_m of any DNA molecule if you know the base composition. The simplest formulas just take the overall composition into account and they are not very accurate. More accurate formula will use the stacking interactions of each base pair to predict the melting temperature [Wikipedia: DNA melting].

The question is why is there a relationship between the base composition of DNA and the stability of the double-stranded regions?

The first people to think about this question didn't really understand the role of stacking interactions between base pairs in the middle of double-stranded DNA. They also didn't really appreciate hydrogen bonds. They naively assumed that the differences between G/C rich DNA and A/T rich DNA was due to the fact that G/C base pairs have three hydrogen bonds and A/T base pairs have only two [The Chemical Structure of Double-stranded DNA].

We now know that this explanation doesn't make sense. There is no net loss of hydrogen bonds when DNA is denatured, quite the reverse in fact. There are more hydrogen bonds formed between the bases in single-stranded DNA and water molecules than between base pairs in DNA. There's no reason why single-stranded DNA would renature if formation of double-stranded DNA was driven by the creation of hydrogen bonds between base pairs. For every hydrogen bond between bases you would have to break almost two hydrogen bonds to water molecules.

The most important interactions in double-stranded DNA are the stacking interactions between adjacent base pairs. You can think of this as the interactions of electrons on the upper and lower surfaces of the rings that form the bases.

There are ten possible interactions between adjacent base pairs. The energies of these interactions are shown in the table on the left. The arrows indicate the direction of the DNA stand from 3′→5′ [The Chemical Structure of Double-Stranded DNA].

Note first of all that the strength of these stacking interactions (about 30 kJ mol^-1 on average) are greater than the strength of stability conferred by hydrogen bonds (about 3 4 kJ mol^-1)¹. Assuming there are on average six three hydrogen bonds per in two stacked G/C base pair, the total strength of the hydrogen bonds (18 12 kJ mol^-1) is still much less than the stacking interactions.

Secondly, note that stacking interactions involving G/C base pairs are stronger (more negative) than those involving A/T base pairs. This is why the melting temperature of DNA depends on the base composition. It's not because G/C base pairs have one more hydrogen bond than A/T base pairs, it's because G/C base pairs form stronger stacking interactions.

This is why you can calculate a more accurate melting temperature for oligonucleotides if you use the stacking interactions. It's stacking interactions that determine the stability of double-stranded DNA and it's stacking interactions that are disrupted as the temperature increases and more thermal energy is added to the molecule.

Finally, the paper that I discussed in July [Measuring Stacking Interactions] measured the stacking interactions in single-stranded DNA (poly A). As it turns out, the stacking interactions between single bases are, in some cases, strong enough to force single-stranded DNA into a helical structure. This is further evidence of the importance of stacking interactions in conferring stability to the double helix.

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1. The stability conferred by each hydrogen bond is the difference between the strength of the bond in double-stranded DNA and its strength in when bonded to water. Hydrogen bonds between bases and water molecules typically have strengths of about 25 kJ mol^-1 and hydrogen bonds between base pairs are a bit higher.

Do Fundamentalist Christians Actively Resist Learning?

 
Last summer Tom Bozzo, an economist in Madison Wisconsin, played around with the latest data on science education in America [Scientific Knowledge in the US by Religion]. He was interested in any correlations between religion and the understanding of basic scientific concepts.

A reader reminded me of this data. It was discussed on several blogs last summer but I had forgotten the details. There's one pair of graphs that are particularly interesting. The first one shows that fundamentalist Protestants, as expected, do not believe that humans evolved whereas atheists—and most other groups—accept the scientific facts.
Tom wanted to know what these results would look like if he only included those respondents with some college education. He cautions us that the numbers are small.
There are several cautions that need to be emphasized. For one thing, there's a relationship between the amount of education one has and the strength of their religious beliefs. Getting an education tends to drive you away from the most fundamentalist religions. That's probably why there's a smaller percentage of college educated fundamentalists (27%) compared to moderates (39%) and liberals (51%). Another problem is that the numbers are small and the associated error bars are large.

Keeping all these cautions in mind, it is still quite remarkable that some significant percentage of fundamentalist Protestants can go to college and still reject the basic scientific fact that humans evolved. Note that in all of the other groups the college educated subset are more inclined to accept evolution. (Do most of those "college" educated fundamentalists go to some cheap reproduction of a college run by a religious organization?)

As we've seen time and time again on the blogs (and elsewhere), the Christian fundamentalists have erected very strong barriers against learning. It really doesn't matter how much they are exposed to rational thinking and basic scientific evidence. They still refuse to listen.

This is one of the reasons why I would flunk them if they took biology and still rejected the core scientific principles. It's not good enough to just be able to mouth the "acceptable" version of the truth that the Professor wants. You actually have to open your mind to the possibility that science is correct and get an education. That's what university is all about.

Of course, we all recognize the problem here. How do you distinguish between a good Christian who is lying for Jesus and one who has actually come to understand science? It seems really unfair to flunk the honest students who admit that they still reject science and pass the dishonest ones who hide their true beliefs.

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"The Twelve Days of Christmas" Is a Secret Catholic Catechism

 
Friday's Urban Legend: FALSE

Today is the fourth day of Christmas (four calling birds). There's a persistent urban legend floating around the internet that the popular song "Twelve Days of Christmas" is actually a secret message about Christianity, made up by persecuted Roman Catholics in England. The story even made it into our local paper (Toronto Star) a few days ago, albeit with a hint that it might not be true.

Here's the 1998 version of the email message.

You're all familiar with the Christmas song, "The Twelve Days of Christmas" I think. To most it's a delightful nonsense rhyme set to music. But it had a quite serious purpose when it was written.

It is a good deal more than just a repetitious melody with pretty phrases and a list of strange gifts.

Catholics in England during the period 1558 to 1829, when Parliament finally emancipated Catholics in England, were prohibited from ANY practice of their faith by law - private OR public. It was a crime to BE a Catholic.

"The Twelve Days of Christmas" was written in England as one of the "catechism songs" to help young Catholics learn the tenets of their faith - a memory aid, when to be caught with anything in writing indicating adherence to the Catholic faith could not only get you imprisoned, it could get you hanged, or shortened by a head - or hanged, drawn and quartered, a rather peculiar and ghastly punishment I'm not aware was ever practiced anywhere else. Hanging, drawing and quartering involved hanging a person by the neck until they had almost, but not quite, suffocated to death; then the party was taken down from the gallows, and disembowelled while still alive; and while the entrails were still lying on the street, where the executioners stomped all over them, the victim was tied to four large farm horses, and literally torn into five parts - one to each limb and the remaining torso.

The songs gifts are hidden meanings to the teachings of the faith. The "true love" mentioned in the song doesn't refer to an earthly suitor, it refers to God Himself. The "me" who receives the presents refers to every baptized person. The partridge in a pear tree is Jesus Christ, the Son of God. In the song, Christ is symbolically presented as a mother partridge which feigns injury to decoy predators from her helpless nestlings, much in memory of the expression of Christ's sadness over the fate of Jerusalem: "Jerusalem! Jerusalem! How often would I have sheltered thee under my wings, as a hen does her chicks, but thou wouldst not have it so..."

The other symbols mean the following:

2 Turtle Doves = The Old and New Testaments
3 French Hens = Faith, Hope and Charity, the Theological Virtues
4 Calling Birds = the Four Gospels and/or the Four Evangelists
5 Golden Rings = The first Five Books of the Old Testament, the "Pentateuch", which gives the history of man's fall from grace.
6 Geese A-laying = the six days of creation
7 Swans A-swimming = the seven gifts of the Holy Spirit, the seven sacraments
8 Maids A-milking = the eight beatitudes
9 Ladies Dancing = the nine Fruits of the Holy Spirit
10 Lords A-leaping = the ten commandments
11 Pipers Piping = the eleven faithful apostles
12 Drummers Drumming = the twelve points of doctrine in the Apostle's Creed

Snopes.com is all over this one [The Twelve Days of Christmas].

There is no substantive evidence to demonstrate that the song "The Twelve Days of Christmas" was created or used as a secret means of preserving tenets of the Catholic faith, or that this claim is anything but a fanciful modern day speculation, similar to the many apocryphal "hidden meanings" of various nursery rhymes. Moreover, several flaws in the explanation argue compellingly against it:

What's interesting about the Snopes.com article is that it explores the real origins of the song and reveals some interesting facts about the corrupted English version.

What we do know is that the twelve days of Christmas in the song are the twelve days between the birth of Christ (Christmas, December 25) and the coming of the Magi (Epiphany, January 6). Although the specific origins of the song "The Twelve Days of Christmas" are not known, it possibly began as a Twelfth Night "memory-and-forfeits" game in which the leader recited a verse, each of the players repeated the verse, the leader added another verse, and so on until one of the players made a mistake, with the player who erred having to pay a penalty, such as a offering up a kiss or a sweet. This is how the song was presented in its earliest known printed version, in the 1780 children's book Mirth Without Mischief. (The song is apparently much older than this printed version, but we do not currently know how much older.) Textual evidence indicates that the song "The Twelve Days of Christmas" was not English in origin, but French. Three French versions of the song are known, and items mentioned in the song itself (the partridge, for example, which was not introduced to England from France until the late 1770s) are indicative of a French origin.

In the original version, the gift on the fourth day was "colly" birds, not "calling" birds. Apparently, "colly" meant black as coal and a "colly bird" was a blackbird. The five "golden rings" refers to ring-necked pheasants. Thus, the first seven gifts are all birds.

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[Image Credit: Cafepres.com]

The Second Grapevine Genome Is Published

 
A second version of the grapevine genome was published at PLoS ONE last week (Velasco et al. 2007). As I began to collect information on that paper I learned that another genome sequence of grapevine had been published independently last September in Nature (Jaillon et al. 2007). Before discussing the PLoS ONE paper I decided to write up a report of that August genome sequence trying to not let the second sequence influence me [The Grapevine Genome].

This gives us an opportunity to evaluate the state of genome biology and genome evolution by comparing two competing analyses of the same genome. Keep in mind that the authors of the second paper were aware of the first study when they published in PLoS ONE so they had an opportunity to correct or modify their own work in light of the previous paper. Thus, the second group is able to point out "errors" in the first sequence and correct "errors" in their own sequence before publication.

Keep this in mind as you read the second paper because it often seems as though the first group to publish did a very sloppy job. What we don't see in the published work is the evidence of sloppiness in the second study that was fixed by referring to the earlier work.

Velasco et al. (2007) also sequenced the Pinot Noir cultivar of Vitis vinifera but unlike the previous study they used a heterogeneous strain. Recall that in the September paper the sequencing team used an inbred line in order to reduce the extreme heterogeneity seen in normal wine-making strains.

The genome size is 505 Mb (505 × 10⁶ bp). This is larger than the earlier published sequence (487 Mb). The extra DNA is almost entirely due to inclusion of ribosomal RNA clusters. Velasco et al. (2007) identified 29,585 genes—only slightly fewer than the 30,434 genes reported by Jaillon et al. (2007). Both teams used fairly strict criteria for identifying and annotating genes. The number of genes in the grapevine genome is comparable to the number in Arabidopsis (26,819) but fewer than the number in poplar (45,555) and rice (41,046). We can expect this number to fall as false positives are eliminated.

There are 719 tRNA genes (including 163 pseudogenes), 89 snRNA genes, and about 1500 copies of the 18S + 5.8S + 28S ribosomal RNA repeat. There are about 175 copies of the 5S RNA gene.

The authors report 166 copies of snoRNA and 143 copies of microRNAs based on known examples in other plant genomes.

Many plants exhibit very high heterogeneity between homologous chromosomes. Sister chromosomes in the Pinot Noir cultivar differ by as much as 11% in DNA sequence, including large gaps. This gives rise to regions that are hemizygous—they contain only one copy of a DNA sequence in a diploid genome. An example of this heterogeneity is shown below.

Two almost contiguous regions of chromosome 1 are depicted. The red regions are transposons of various kinds (c=Copia, a=Gypsy/athila, etc.). You can see that many of the deletions/insertions are at transposon positions indicating that much of the heterogeneity between sister chromosomes is due to the insertion and excision of active transposons. This level of transposon activity is rare in mammalian genomes but common in flowering plants.

In order to study the evolution of the grapevine genome, Velasco et al. (2007) compared the sequences of paralogous genes. These are genes that belong to a gene family that diverged from a common ancestor. By comparing the differences in sequence between any two genes it is possible to estimate the time of divergence. In order to avoid any bias due to selection, it is preferable to only compare nucleotide substitutions that do not change the amino acid sequence (synonymous substitutions, K_s).

The results are shown in the figure above. Most of the pairs of genes are very similar with 0 or 0.1 substitutions. These genes arose from a very recent duplication event. There is a secondary peak at about 0.9 substitutions indicating that a large number of genes were duplicated at some particular time in the past. If this is evidence of a genome-wide duplication event then these pairs of genes should be clustered in syntenic regions. (Large segments of the chromosome that have the same order of genes.)

The insert (E) shows the distribution of those pairs from syntenic regions. It looks like most of the pairs have accumulated similar numbers of substitutions suggesting strongly that there was a genome-wide duplication event.

It is well known that flowering plant genomes have undergone polyploidization and/or hybridization during their evolution from a common ancestor about 200-300 million years ago. In their September paper in Nature, Jaillon et al. (2007) proposed that the grapevine genome was closer to the common ancestor of dicotyledenous plants. Their analysis suggested that all dicots arose from a hexaploid ancestor (three haploid genome equivalents). Further duplications occurred in the lineages leading to poplar and Arabidospis, according to Jaillon et al. (2007) [The Grapevine Genome].

Velasco et al. (2007) disagree. In the second genome study they claim that the ancestral dicot genome was tetraploid (one round of duplication) and that a second round of duplication (2R) occurred in the grapevine lineage after it diverged from poplar and Arabidopsis (see below). Note that in this study Arabidopsis and poplar are assumed to more closely related to each other than they are to grapevine whereas in the previous study grapevine was clustered with poplar.



A third duplication (3R) took place independently in the lineages leading to Arabidopsis and polar, according to Velasco et al. (2007).

At present, it isn't possible to say who is correct. In fact, they might both be wrong. The significance of these two studies is that it gives us some idea of the level of confidence we can place on speculations about genome evolution. How you interpret your data depends very much on how you compare sequences both within a species and between species. The data does not seem to be good enough to make confident predictions as judged by the differing opinions of these two groups.

The take-home lesson is that we need to take studies of this sort with a large grain of salt. In most cases we won't be lucky enough to have competing labs to analyze the same data and point out differing interpretations.

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