The Evolution of the HSP70 Gene Family

Here's a picture of my three second year project students in front of their poster. Blerta Kolaj, Milu Jauregui, and Zarna Shah collaborated on this project to study the evolution of various members of the HSP70 gene family.

Eukaryotes contain at at least five or six versions of HSP70 genes. Two of them are present in single copies (mostly) and they were present in the common ancestor of all eukaryotes. One of these is the mitochondrial version, which is derived from the proteobacterium ancestor of mitochondria. The other is a version found in the endoplasmic reticulum (ER). The ER member of the HSP70 gene family (=BiP) arose very early in eukaryotic evolution.

A phylogenetic tree of either the mitochondrial gene or the ER gene should reveal the evolution of all eukaryotic species. The two trees should be identical provided the genes evolve independently and there has been no horizontal gene transfer. Furthermore, the two trees will root each other since they join at a common ancestral node representing the split between eukaryotes and prokaryotes. The purpose of the experiment is to test this hypothesis and see if we have enough examples of ER and mitochondrial genes to make duplicate trees. The problem is that we need an example of each gene in every species we test. The fact that we now have quite a few genome sequences means that this has become more feasible than in the past.

Blerta, Milu, and Zarna were able to add in one more set of sequences; the chloroplast members of the HSP70 gene family. These genes are derived from the cyanobacteria ancestor of chloroplasts so they provide independent confirmation of the eukaryotic tree for plants and algae. Unfortunately, there aren't very many examples of species that have sequenced versions of the chloroplast gene, the mitochondrial gene, and the ER gene.

Here's the tree.

As you can see, the relationship of most species (actually genes) in the mitochondrial and ER branches is very similar. This confirms that the two family members are evolving independently. Differences occur with the protists such as trypanosomes, Leishmania, plasmodia, and cryptosporidium. This is unfortunate since analysis of HSP70 genes could have helped resolve the relationship of protists, which is very controversial. At least we're sure of the roots of each major branch—that's a big step forward.

The chloroplast and mitochondrial clades are closer together than either is to the eukaryotic ER versions of the HSP70 family. This is not unexpected since both organelle genes are prokaryotic in origin. It suggests that the universal root is along the branch leading to the ER clade.

Now my students have to turn their attention to their individual projects. They have about six weeks to finish up. I'll post summaries of their work in May. I'm pretty excited about all three projects, we could end up answering some pretty important questions using the HSP70 database.

Sandwalk DNA Fingerprint

 


Here's the Sandwalk DNA fingerprint from web2dna.

[Hat Tip: ScienceRoll]

Not Banned in China

 


My blog is not (yet) banned in China! Test your own site at Great Firewall of China.

[Hat Tip: ScienceRoll]

Me and Steve

 
Here's a picture of me and Steve Steve in North Carolina. That Steve sure gets around. At times he seems to be in two or three places at once.

Now that I think of it, this Steve doesn't look the same as the one I met in San Francisco. You don't suppose there's two of them, do you?

Could it be that the Steve Creator has learned how to clone?

Lunar Eclipse

 
Looks like we're going to miss the total lunar eclipse because of the clouds. Oh well, they're not that rare so another will come along in a few months.

Lunar eclipses come in bunches with periods of drought in between. The last one was on October 28, 2004 so it seems like a long time has passed for those who have been waiting. The good news is that there will be two more in the next year.

When they occur, a lunar eclipse can be viewed by more than half the planet. One of the unusual things about this one is that it can be seen by people on every continent. That's just a question of timing.

Some newspaper reports are saying that lunar eclipses are "rare." I suppose it depends on your perspective. To me "rare" means once or twice in a lifetime so I wouldn't say that lunar eclipses are "rare." Total solar eclipses, on the other hand are rare for any individual place on the planet.

For more information on lunar eclipses see the Sky and Telescope website [March 3rd's Total Lunar Eclipse]. I'm including a copy of their diagram to show you how lunar eclipses work. Pay attention if you're a university student 'cause it may be on the University Exit Exam.

This What Happens to your Brain on Religion

 
See this man? His name is Nathan Bradfield. He is associated with Gateway Baptist Church in Montgomery Alabama.

That makes him an expert on evolution. He has a blog. He has posted an article called Hypocrisy of Evolution. He quotes many experts, like Ann Coulter. She is an IDiot. So is Nathan.

Kevin Beck says this is Easily the worst anti-evolution blogging any of us have seen. Maybe it is. Kevin invites you to pick a sentence, any sentence, and show why it's wrong. Not much of a challenge.


I didn't like this when it was an anti-drug commercial but it seems appropriate for what (some) religion can do to your brain.

Atheists and Agnostics

 
Here's a list of various countries with the percentage of atheists + agnostics. In most cases the total comes from the number who self-identify as people who do not believe in God. The number who feel comfortable labeling themselves as atheists is usually about 1/4 of the total.

The data is mostly from ...

Zuckerman, P. (2005) "Atheism: Contemporary Rates and Patterns ", chapter in The Cambridge Companion to Atheism, ed. by Michael Martin, Cambridge University Press: Cambridge, UK

Greeley, A. (2003) Religion in Europe at the End of the Second Millennium. New Brunswick, NJ: Transaction Publishers

It is summarized on the Adherent Statistics website.

Australia Canada Czech Republic France Germany Israel Italy Netherlands Norway Poland Russia Saudi Arabia Spain Sweden United Kingdom United States

25% 19% 54% 48% 35% 37% 18% 43% 41% 8% 35% 0% 18% 46% 44% 4%

Norris and Inglehart (2004) Bibby (2002) Greeley (2003) Greeley (2003) Greeley (2003) Kedem (1995) Greeley (2003) Greeley (2003) Greeley (2003) Greeley (2003) Froese (2004) Zuckerman (2005) Greeley (2003) Greeley (2003) Zuckerman (2005) Encyclopedia Britannica

Sound the Alarm! Liechtenstein Invaded!

 
FOXNews reports on the invasion of Liechtenstein.

ZURICH, Switzerland — What began as a routine training exercise almost ended in an embarrassing diplomatic incident after a company of Swiss soldiers got lost at night and marched into neighboring Liechtenstein.

According to Swiss daily Blick, the 170 infantry soldiers from the neutral country wandered more than a mile across an unmarked border into the tiny principality early Thursday before realizing their mistake and turning back.

A spokesman for the Swiss army confirmed the story, but said that there were unlikely to be any serious repercussions for the mistaken invasion.

"We've spoken to the authorities in Liechtenstein and it's not a problem," Daniel Reist told The Associated Press on Friday.

Officials in Liechtenstein also played down the incident.

Interior Ministry spokesman Markus Amman said nobody in Liechtenstein had even noticed the soldiers, who were carrying assault rifles but no ammunition. "It's not like they stormed over here with attack helicopters or something," he said.

Liechtenstein, which has about 34,000 inhabitants and is slightly smaller than Washington, D.C., does not have an army.

Read this carefully. Liechtenstein doesn't have an army. The border wasn't marked. The Swiss soldiers had assault rifles but no ammunition. Only in Europe .... that's what a lack of religion leads to.

Be Like PZ

 
Just in case there are one or two people out there who don't read Pharyngula every day, here's the latest from PZ Myers: Get meaner, angrier, louder, fiercer. He has little use for appeasers and fencesitters.

Aspartame Is Poisonous

Friday's Urban Legend: FALSE

The idea that aspartame is poison is widespread—much more common than most rational people would care to admit. You can hear people whispering about the dangers of aspartame in the coffee shops and on the commuter trains. If you believe what they're saying then aspartame is one of the most poisonous products that has ever been foisted on the public by unscrupulous international corporations. It's part of a vast conspiracy to murder innocent citizens in the name of corporate profit. This sort of thing is just a small part of a growing belief in all kinds of irrational, superstitious nonsense that threatens to make a mockery of science.

Here's a typical claim from a site called "Ethical Investing" (sic).

The artificial sweetener aspartame (NutraSweet, Equal, NatraTaste, Canderel) is without question the most toxic and health-destroying "food" sold to consumers. The number of people who have recognized toxicity reactions or damage from chronic aspartame ingestion is well over one million people in the U.S. (based on the reported toxicity reactions divided by the estimated reporting rate). While many people's health has already been destroyed by this product, the more serious concern is the long-term nervous system damage, immune system damage, and irreversible genetic damage known to be caused by aspartame's metabolite, formaldehyde. Formaldehyde can cause severe health problems at exceptionally low levels of exposure.

Here's another, from a website called "The Light Party."

Diet Coke is poison. And it's addictive, some victims drink several liters a day and keep it on their nightstands. If Coke changes the formula to remove aspartame the world will heal and the surge of hatred and vengeance by the disabled and bereaved shall certainly destroy Coca Cola.

The poison in Diet Coke is aspartame. As a member of the National Soft Drink Association Coke opposed FDA approval of aspartame for beverages. their objections, running to several pages published in the Congressional Record of 5/7/85, said aspartame is uniquely and inherently unstable and breaks down in the can. It decomposes into formaldehyde, methyl alcohol, formic acid, diketopiperazine and other toxins. In a study on 7 monkeys 5 had grand mal seizures and one died, a casualty rate of 86%.

This is all nonsense. The false claims are countered by dozens of scientific studies that show no adverse effects of aspartame. Snopes.com has a summary at Kiss My Aspartame.

[In a sop to the superstitious, you can also buy Diet Coke sweetened with SPLENDA®]

A Sophisticated Christian Philosopher Critiques The God Delusion

 
Richard Dawkins is often accused of being naive. Some of his fiercest critics are moderate Christians who claim that the religion Dawkins attacks is not their religion. The claim is that Dawkins is attacking a strawman version of Christianity and not the real intellectually sophisticated version that they believe in.

This form of criticism is called the Courtier's Reply an amazingly apt response invented by PZ Myers.

Now, one of the "really sophisticated" Christians has posted a review of The God Delusion. Alvin Plantinga is Professor of Philosophy at the University of Notre Dame. It will be interesting to see how a believer in modern sophisticated Christianity performs. Jason Rosenhouse dissects the review at Evolutionblog (Plantinga on Dawkins: Part One). It doesn't look good. Superstition is superstition no matter how you dress it up.

Jerry Falwell Promotes Superstition

 
In the ongoing battle against superstition it helps from time to time to point out the greatest offenders. I'm not exactly sure how the Neville Chamberlain Atheists approach this issue but for me it's very clear. Stupid, superstitious, idiots like Jerry Falwell need to be exposed and opposed. The fact that they are Christian fundamentalists is a bonus.

Here's the latest from Falwells' sermon last week (THE MYTH OF GLOBAL WARMING).

In recent years, since Al Gore invented the internet and helped invent global warming, our world has been in turmoil. The internet turned out to be “a very good thing” and, when used properly, is a great asset to humanity.

The endless hysteria and alarmism over alleged global warming has increasingly become a national and international nuisance and loses credibility with every passing day. The entire myth has little to do with science and much to do with politics.

Its greatest proponents are the United Nations (no friends of America), liberal politicians, radical environmentalists, liberal clergymen, Hollywood and pseudo-scientists.

Didn't he forget gays? Was that a delberate oversight?

It should be expected that liberal clergymen and theologians would join in concert with Hollywood and liberal politicians on every radical and hurtful issue that arises. But, sadly, some evangelical pastors and leaders have recently jumped aboard this brand new bandwagon. This bandwagon is not abortion, school prayer or gay marriage… rather, it’s a cause that former VP Al Gore is championing in his film, “An Inconvenient Truth” (better named “a Convenient Untruth”: namely global warming.

Whew! That's a relief. He managed to slip gays into the next paragraph. For a minute I thought he was losing it.

What does the Bible say about a global warming catastrophe that will melt the glaciers, raise the sea levels to horrific destructive heights and eliminate the four seasons beyond any recognizable difference.

Psalm 24:1-2, “The earth is the LORD's, and the fulness thereof; the world, and they that dwell therein. 2 For he hath founded it upon the seas, and established it upon the floods.”

Genesis 8:22, “While the earth remaineth, seedtime and harvest, and cold and heat, and summer and winter, and day and night shall not cease.”

I'm not sure what this means. Does it mean that the coming rise in sea level will be God's fault because He did it once before?

Words from a Proud Neville Chamberlain Atheist

 
Chris is a cognitive psychologist (Mixing Memory). He claims to be a proud Neville Chamberlain atheist. He writes about Religion and Social Critique.

While I think it's obvious to anyone with eyes (a category that seems to grow smaller by the day) that within the anti-religious bigotry today there is an underlying feeling of superiority, an unliberal belittling of the little guy, a feeling that "Joe Schmoe" is stupid and to some extent worth less than the intellectually righteous secularist, ...

Whoa! I think he's talking 'bout people like me here. First of all, I'm not a bigot. If you want to have an intelligent discussion about rationalism and superstition then it's best to avoid that term unless you can back it up. Second, I do feel strongly that my opinion is better than contrary opinions. Are there any other possibilities? Are there some people who feel that their opinions are unworthy? Thirdly, some of the people who believe in superstitious nonsense really are stupid. And they really are bigots—yes, I can back that up.

(Incidentally, I'm sure that in the interests of fairness, Chris has posted a strong criticism of the bigotry and intolerance of religious leaders in the USA. I look forward to getting the URL to those postings.)

... there is another element to rabid atheist criticisms of religion that I find both disturbing and puzzling. As many of the comments to my recent post and Pharyngula's post on the same topic illustrate, these criticisms of religion are largely based on its perceived social and political effects. That is, the critique of religion by these atheists (let's call them Churchillians) is a social critique.

Oh, that's a relief. It's not me he's referring to. My criticism of religion is based on the idea that its supporters believe in supernatural beings. That's a delusion because there's no evidence of supernatural beings. The fact that some religions are sexist, racist, and homophobic is incidental. I'm well aware of the fact that this doesn't apply to all religions. I'm equally opposed to the more liberal versions of religion because the underlying premise is wrong, in my opinion.

This is the part that Chris and his fellow appeasers don't get. They oppose the extreme versions of religion because of the outward manifestations of social behavior. But they give a free pass to all those superstitions that don't recruit suicide bombers or put women in the back pews. I don't make that distinction. To me the battle is between rationalism and superstition. The social critique is secondary.

What I find disturbing and puzzling about it is its naïveté. As I believe fellow ScienceBlogger and Chaimberlainian atheist Razib has pointed out before (I don't have a link right now, but if he gives me one, I'll add it later), religion is such an effective user of our cognitive and social composition that it falls naturally out of them. So naturally, in fact, that there is no reason to believe that religion is going away, much less that it is possible, through accusation and invective, to facilitate religion's demise. In other words, as social critiques go, the Churchillians' is about as ineffective as you'll find.

Chris, I'll let you in on a little secret. I don't hide my light under a bushel just because I think my chances of changing the world are slim. So, even if it were true that the USA will always be strongly religious that wouldn't be a reason to keep quiet. I don't believe that America is going to accept gays and lesbians anytime soon but that's not a reason to give up the fight. Or, do you think it is? Do you advocate an appeaser position toward homophobic bigots on the grounds that you'll never change their minds?

But, setting the illogic of your argument aside, let's think about the future of religion. European societies became more and more secular in the 20th century. Canada is much, much less religious than the USA. Do you really think that America will resist the change? I don't. Furthermore, I think your statement that the "Churchillians" are being ineffective is patently absurd. Richard Dawkins has done more to stimulate debate about atheism than hundreds of appeasers. Although you misrepresent his position, the fact is that by being blunt he has got people's attention and that's the first step toward getting them to question their beliefs.

Would it not be better to recognize that the content of specific religions has, historically, varied according to the spirit of the times, and therefore the most effective avenue for social critique is to focus on changing that spirit, thereby necessarily effecting change in the content of religion? If you want to make the religious less intolerant, and less hostile towards members of outgroups, wouldn't it be better to work towards a society that is itself less intolerant and hostile towards members of outgrups?

Yes, if your only goal is to make people more tolerant then that's what you should do. Meanwhile, some of us are trying to get people to abandon superstition—that's a different goal.

In other words, it seems to me that the problem with the Churchillian critique is that it mistakes a symptom for the cause; it fails to recognize that religions are, as they have always beens (and as any social institutions are and will alway be), tools of power and domination, and that the object of critique should be the powerful and the dominant.

Wrong. It is you who is making the mistake. The "Churchillians" are opposed to superstition because it's not rational. We don't distinguish between superstitions that are associated with intolerance and those that aren't. Why is this so difficult to understand?

I think, for example, of the ways in which religion and society changed together in 18th century Europe, or the differences between the focus and attitudes of the religious in many European countries as opposed to the United States today. Religions that have survived for millennia have done so because they are incredibly adaptive, and it is the responsibility of anyone with a progressive world-view, recognizing that religion will not go away, to force religion to change by changing its environment and thereby forcing it to adapt. Calling religious people stupid, and treating religion as inherently evil, simply won't accomplish that.

My goal is to achieve a society where there is no religion. I want people to stop believing in supernatural beings for which there is no evidence. I would also like to live in a society with a "more progressive world-view." Both goals are achievable. We don't want an atheistic intolerant society any more than we want a religious intolerant society.

A State of Extreme Cognitive Dissonance

Poor old GilDodgen. He's really suffering over his inability to understand some basic biochemistry [Yet Another Irreducible Complexity No-Brainer — Twisted Ropes]. Naturally, he interprets his ignorance to be proof that Intelligent Design Creationism has the answers.

Watch this video to see why GilDodgen is in a state of extreme cognitive dissonance.



Here's what GilDodgen says after watching the video ...

I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone. This might make for another highly persuasive ID mascot.

You are right to start looking around for another mascot since protein synthesis and the bacterial flagellum aren't working for you. But you better be careful about adopting a new poster girl. Maybe you should learn some basic biochemistry before you end up looking even more stupid than usual. Reading a textbook would help.

How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension? What would be the functional, naturally-selectable intermediate steps in a hypothetical stochastically generated evolutionary process? It is clear that there could not possibly be any.

Here's a picture of E. coli topoisomerase I bound to DNA. The mechanism of action of this enzyme is well known. There are four basic steps.

In step I, the enzyme binds to a single-stranded bubble region of DNA. Such regions are characteristic of supercoiled DNA. The enzyme then cuts the DNA in an endonuclease reaction that's often referred to as a "nickase" activity. There are dozens of endonucleases that can carry out this reaction. They are required for DNA replication, repair, and recombination and they evolved for that purpose. Topoisomerases evolved from such nickases.

In step 2, one end of the cleaved DNA is covalently attached to the enzyme via a phosphotyrosince bond. This is likely to be the single evolutionary invention of topoisomerases, although there are other enzymes that have covalently attached nucleic acids. The covalent attachment means that the enzyme remains firmly bound to the site of the nick where it will catalyze a resealing reaction.

In step 3, the other stand of DNA passes through the site of the nicked strand. This is a simple consequence of the fact that the enzyme is holding on to the ends of the cleaved strand.

In step 4, the enzyme catalyzes rejoining of the two ends. This is a ligase reaction. There are dozens of known ligases. They are required for DNA replication, repair, and recombination and they evolved independently to faciliate those reactions. Topoisomerases combine the activities of an endonuclease and a ligase in a single protein but these activities arose originally as separate enzymes. (This was probably a gene fusion event—there are dozens of examples of gene fusions where seprate enzyme activities are brought together in a single protein.)

So the evolution of topoisomerases goes like this. In the beginning, separate nicking enzymes and ligase enzymes were all that was required to relieve tension in front of a replication fork. Over time these two activities became combined in a single enzyme that could quickly bind to DNA under tension, nick one strand, allow free rotation around the other strand, and reseal the nick.

The advantage of having a single enzyme do what used to require two separate enzymes is that the nicking-resealing steps could be faster and this allowed for faster DNA replication. That's probably why there was selection for an enzyme with both activites that didn't let go of DNA.

The last step in the evolution of topoisomerases was selection for the covalent attachment of DNA to the enzyme. This allowed for the possibility of topoisomerase binding to regions that were not under torsional stress in order to relieve supercoils. This, in turn, paved the way for the evolution of much longer DNA strands and circular forms of DNA that could store supercoils. Since supercoiling is related to packaging DNA, this also contributed to the evolution of larger genomes.

I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what is now known about the nature of living systems (at all levels, not just the biochemical)?

I don't have much trouble coming up with a defense of the "indefensible." But then I have a huge advantage over GilDodgen because I'm a scientist and, as he says, scientists are intelligent and educated.

Evolution Is a Fact

DaveScot over at Uncommon Descent writes in Theory of Evolution as well tested as…,

We often hear biologists claim the theory of evolution is as well tested as the theory of gravity.

No, you don't, DaveScot. That's not what you hear at all. You aren't listening. (Either that or you're lying but I'd rather give you the benefit of the doubt even though you're an IDiot.)

What biologists say is that Evolution Is a Fact and a Theory. Gravity is a fact just like evolution. That's what you hear biologists saying. The "Theory of Gravity" and "Evolutionary Theory" are something completely different from facts. It may even be the case that evolutionary theory is on more solid grounds than the theory of gravity.

Let me remind all IDiots of what Stephen J. Gould said 26 years ago. Study these words. It will prevent you from looking stupid in the future.

In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is "only" a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science—that is, not believed in the scientific community to be as infallible as it once was."

Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered.

Moreover, "fact" doesn't mean "absolute certainty"; there ain't no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional consent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory—natural selection—to explain the mechanism of evolution.

Stephen J. Gould, " Evolution as Fact and Theory"; Discover, May 1981