Wednesday, June 25, 2008

Conservapedia gets Schooled.

So, some of you may have heard of Andrew Schlafly, who once described his Conservapedia as "unbiased, from a conservative viewpoint." Classy.

At any rate, their own website chronicles the effective ripping apart of an attempt by Schlafly of the rather elegant work done by Richard Lenski, who, for the last several years, has done long-term studies on the evolution of E. coli. In particular, he managed to breed E. coli which is capable of growing in a media where the only available food source is citrate, a food source not normally used by E. coli. He showed that this was a novel pathway in these bacteria which was not present in their ancestral population. He even identified the mutations necessary to bring it about.

Anyhow, I can't guarantee how long this page will remain up. Conservapedia has a way of censoring their own website, but will include a link to Dr. Lenski's demolishing of Schlafly's attacks, and I want to include here, the full text of Lenski's final response.

Dear Mr. Schlafly:

I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content. Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite. I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

First, it seems that reading might not be your strongest suit given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you still had not bothered to read our paper. You wrote: “I did skim Lenski’s paper …” If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?

Second, your capacity to misinterpret and/or misrepresent facts is plain in the third request in your first letter, where you said: “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.” That statement was followed by a link to a news article from NewScientist that briefly reported on our work. I assumed you had simply misunderstood that article, because there is not even a mention of proteins anywhere in the news article. As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.” So where did your confused assertion come from? It appears to have come from one of your earlier discussions, in which an acoltye (Able806, who to his credit at least seems to have attempted to read our paper) wrote:

“I think it might be best to clarify some of Richard's work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at PNAS is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony. ...”

As further evidence of your inability to keep even a few simple facts straight, you later wrote the following: “It [my reply] did clarify that his claims are not as strong as some evolutionists have insisted.” But no competent biologist would, after reading our paper with any care, insist (or even suggest) that “3 new and useful proteins appeared in the colony around generation 20,000” or any similar nonsense. It is only in your letter, and in your acolyte’s confused interpretation of our paper, that I have ever seen such a claim. Am I or the reporter for NewScientist somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?

Third, it is apparent to me, and many others who have followed this exchange and your on-line discussions of how to proceed, that you are not acting in good faith in requests for data. From the posted discussion on your web site, it is obvious that you lack any expertise in the relevant fields. Several of your acolytes have pointed this out to you, and that your motives are unclear or questionable at best, but you and your cronies dismissed their concerns as rants and even expelled some of them from posting on your website. [Ed.: citation omitted due to spam filter] Several also pointed out that I had very quickly and straightforwardly responded that the methods and data supporting the evolution of the citrate-utilization capacity are already provided in our paper. One poster in your discussions, Aaronp, wrote:

“I read Lenski's paper, and as a trained microbiologist, I thought that it was both thorough and well done. His claims are backed by good data, namely that which was presented in the figures. I went through each of the figures after Aschlafly said that they were uninformative. Actually, they are basic figures that show the population explosion of the bacterial cultures after the Cit+ mutation occurred. These figures show that the cultures increased in size and mass at a given timepoint, being able to do so because they had evolved a mechanism to utilize a new nutrient, without the assistance of helper plasmids. ... Lenksi’s paper, while not the most definite I’ve seen, is still a very well-researched paper that supports its claims nicely.”

(As far as I saw, Aaronp is the only poster who asserted any expertise in microbiology.) As further evidence of the absence of good-faith discussion about our research, in the discussion thread that began even before you sent your first email to me, I counted the words “fraud” or “fraudulent” being used more than 10 times, including one acolyte, TonyT, who says bluntly that I am “clearly a fraudulent hack.” In the discussion thread that also includes comments after my first reply, the number of times those same words are used has increased to 20, with the word “hoax” also now entering the discussion. A few posters wisely counseled against such slander but that did not deter you. I must say, it is surprising that someone with a law degree would make, and allow on his website, so many nasty comments that implicitly and even explicitly impugn my integrity, and by extension that of my collaborators, without any grounds whatsoever and reflecting only your dogmatic adherence to certain beliefs.

Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say “data not shown”, which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. []

One of your acolytes, Dr. Richard Paley, actually grasped this point. He does not appear to understand the practice and limitations of science, but at least he realizes that we have the bacteria, and that they provide “the real data that we [that’s you and your gang] need”. Here’s what this Dr. Paley had to say:

“I think there’s a great deal of misunderstanding here from the critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski and his supporters. The real data that we need are not in the paper. Rather they are in the bacteria used in the experiments themselves. Prof. Lenski claims that these bacteria ‘evolved’ novel traits and that these were preceded by the evolution of ‘potentiated genotypes’, from which the traits could be ‘reevolved’ using preserved colonies from those generations. But how are we to know if these traits weren’t ‘potentiated’ by the Creator when He designed the bacteria thousands of years ago, such that they would eventually reveal themselves when the time was right? The only way this can be settled is if we have access to the genetic sequences of the bacteria colonies so that we can apply CSI techniques and determine if these ‘potentiated genotypes’ originated through blind chance or intelligence. But with the physical specimens in the hands of Darwinists, who claim they will get around to the sequencing at some unspecifed future time, how can we trust that this data will be forthcoming and forthright? Thus, Prof. Lenski et al. should supply Conservapedia, as stewards, with samples of the preserved E. coli colonies so that the data can be accessible to unbiased researchers outside of the hegemony of the Darwinian academia, even if it won’t be put to immediate examination by Mr. Schlafly. This is simply about keeping tax-payer-funded scientists honest.”

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate. A competent microbiologist, perhaps requiring the assistance of a competent molecular geneticist, would readily confirm the following properties reported in our paper: (i) The ancestral strain does not grow in DM0 (zero glucose, but containing citrate), the recipe for which can be found on my web site, except leaving the glucose out of the standard recipe as stated in our paper. (ii) The evolved citrate-using strain, by contrast, grows well in that exact same medium. (iii) To confirm that the evolved strain is not some contaminating species but is, in fact, derived from the ancestral strain in our study, one could check a number of traits and genes that identify the ancestor as E. coli, and the evolved strains as a descendant thereof, as reported in our paper. (iv) One could also sequence the pykF and nadR genes in the ancestor and evolved citrate-using strains. One would find that the evolved bacteria have mutations in each of these genes. These mutations precisely match those that we reported in our previous work, and they identify the evolved citrate-using mutants as having evolved in the population designated Ara-3 of the long-term evolution experiment, as opposed to any of the other 11 populations in that experiment. And one could go on and on from there to confirm the findings in our paper, and perhaps obtain additional data of the sort that we are currently pursuing.

Before I could send anyone any bacterial strains, in order to comply with good scientific practices I would require evidence of the requesting scientist’s credentials including: (i) affiliation with an appropriate unit in some university or research center with appropriate facilities for storing (-80ÂșC freezer), handling (incubators, etc.), and disposing of bacteria (autoclave); and (ii) some evidence, such as peer-reviewed publications, that indicate that the receiving scientist knows how to work with bacteria, so that I and my university can be sure we are sending biological materials to someone that knows how to handle them. By the way, our strains are not derived from one of the pathogenic varieties of E. coli that are a frequent cause of food-borne illnesses. However, even non-pathogenic strains may cause problems for those who are immune-compromised or otherwise more vulnerable to infection. Also, my university requires that a Material Transfer Agreement be executed before we can ship any strains. That agreement would not constrain a receiving scientist from publishing his or her results. However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

I would also generally ask what the requesting scientist intends to do with our strains. Why? It helps me to gauge the requester’s expertise. I might be able to point out useful references, for example. Moreover, as I’ve said, we are continuing our work with these strains, on multiple fronts, as explained in considerable detail in the Discussion section of our paper. I would not be happy to see our work “scooped” by another team – especially for the sake of the outstanding students and postdocs in my group who are hard at work on these fronts. However, that request to allow us to proceed, without risk of being scooped on work in which we have made a substantial investment of time and effort, would be just that: a request. In other words, we would respect PNAS policy to share those strains with any competent scientist who complied with my university’s requirements for the MTA and any other relevant legal restrictions. If any such request requires substantial time or resources (we have thousands of samples from this and many other experiments), then of course I would expect the recipient to bear those costs.
So there you have it. I know that I’ve been a bit less polite in this response than in my previous one, but I’m still behaving far more politely than you deserve given your rude, willfully ignorant, and slanderous behavior. And I’ve spent far more time responding than you deserve. However, as I said at the outset, I take education seriously, and I know some of your acolytes still have the ability and desire to think, as do many others who will read this exchange.

Richard Lenski

P.S. Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10^20 = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

P.P.S. I hope that some readers might get a chuckle out of this story. The same Sunday (15 June 2008) that you and some of your acolytes were posting and promoting scurrilous attacks on me and our research (wasn’t that a bit disrespectful of the Sabbath?), I was in a church attending a wedding. And do you know what Old Testament lesson was read? It was Genesis 1:27-28, in which God created Man and Woman. It’s a very simple and lovely story, and I did not ask any questions, storm out, or demand the evidence that it happened as written at a time when science did not yet exist. I was there in the realm of spirituality and mutual respect, not confusing a house of religion for a science class or laboratory. And it was a beautiful wedding, too.

P.P.P.S. You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

P.P.P.P.S. I noticed that you say that one of your favorite articles on your website is the one on “Deceit.” That article begins as follows: “Deceit is the deliberate distortion or denial of the truth with an intent to trick or fool another. Christianity and Judaism teach that deceit is wrong. For example, the Old Testament says, ‘Thou shalt not bear false witness against thy neighbor.’” You really should think more carefully about what that commandment means before you go around bearing false witness against others.

We scientists have been playing softball with creationists for long enough. I think it's about time we started hitting back.

Tuesday, June 24, 2008

How Genesis 1 should read.

Chapter 1

1. In the beginning God created Dates.

2. And the date was Monday, September 7th, 4177 BC.

3. And God said, let there be light; and there was light. And when there was Light, God saw the Date, that it was Monday, and he got down to work; for verily, he had a Big Job to do.

4. And God made pottery shards and Silurian mollusks and pre-Cambrian limestone strata; and flints and Jurassic Mastodon tusks and Picanthopus erectus skulls and Cretaceous placentals made he; and those cave paintings at Lasceaux. And that was that, for the first Work Day.

5. And God saw that he had made many wondrous things, but that he had not wherein to put it all. And God said, Let the heavens be divided from the earth; and let us bury all of these Things which we have made in the earth; but not too deep.

6. And God buried all the Things which he had made, and that was that.

7. And the morning and the evening and the overtime were Tuesday.

8. And God said, Let there be water; and let the dry land appear; and that was that.

9. And God called the dry land "land;" and the water called he the Sea. And in the land and beneath it put he prehistoric carboniferous forests yielding anthracite and other ligneous matter; and all these called he Resources; and he made them Abundant.

10. And likewise all that was in the sea, even unto two hundred miles from the dry land, called he resources; all that was therein, like manganese nodules, for instance.

11. And the morning unto the evening had been a long day; which he called Wednesday.

12. And God said, Let the earth bring forth every moving creature, with or without wings or feet, or fins or claws, vestigial limbs and all, right now; and let each one be of a separate species. For lo, I can make whatsoever I like, whensoever I like. But he didst verily also make ring species, just to confuse matters.

13. And the earth brought forth abundantly all creatures, great and small, with and without backbones, with and without wings and feet and fins and claws, vestigial limbs and all. And verily were ring species made, just to confuse matters.

14. But God blessed them all, saying, Be fruitful and multiply and Evolve Not.

15. And God looked upon the species he hath made, and saw that the earth was exceedingly crowded, and he said unto them, Let each species compete for what it needed; for Competition is My Law. And the species competeth, the cattle and the creeping things; and the dogs ate the brontosauruses and God was pleased. And grass didst verily outrun the velociraptors, and God was pleased.

16. And God took the bones from the dinosaurs, and caused he they to appear old; and cast he them about the land and the sea. And he took every tiny creature that hadst been eaten by dogs, and which hadst not survived the Competition, and caused them to become fossils; and cast he them about likewise.

17. And just to put matters beyond the valley of the shadow of a doubt God created radiometric dating, and didst verily set the ratio of radioactive isotopes to make the world appear mightily old.

18. And in the Evening of the day which was Thursday, God saw that he had put in another good day's work.

19. And God said, Let us make man in our image, after our likeness, which is tall and well-formed and pale of hue: and let us also make apes, which resembleth us not in any wise, but are short and ill-formed and hairy. And God added, Let man have dominion over the monkeys and the fowl of the air and every species.

20. So God created Man in His own image; tall and well-formed and pale of hue created He him, and nothing at all like the apes. And verily didst God create Endogenous Retroviruses and transposons. And placed they he these in Humans and all apes, which resembleth Man not at all.

21. And created He the redundant pseudogenes, such as the Hemoglobin pseudogene, and placed they he in the genome in the exact chromosomal location in all Humans which corresponds to the Apes, even though they resembleth us not at all.

22. And verily didst He break the gene for Vitamin C synthesis, and placed it verily within the genome for Humans, as well as apes which resembleth us not at all. For Scurvy was His will, but only for Humans and Apes and Monkeys, even though they resembleth us not at all.

24. And God saw everything he had made, and he saw that it was very good; and God said, It just goes to show Me what the private sector can accomplish. With a lot of fool regulations this could have taken billions of years.

25. And the evening of the fifth day, which had been the roughest day yet, God said, Thank me it's Friday. And God made the weekend.

Monday, June 23, 2008

Get Intelligent Design into the Classroom in 6 easy steps

1. Actually come up with a theory of Intelligent Design. It must make positive, testable predictions beyond "Evolution is wrong, therefore Intelligentdesignerdidit." It must make predictions of the form "if intelligentdesignerdidit, then when we perform experiment x, we will observe y." Observing something other than y must disprove the theory of Intelligent Design.

2. Perform experiments. The results of those experiments must not be explainable by the theory of evolution, or by any other explanation other than an intelligent designer. In the course of these experiments, you must make a concerted effort to conclusively disprove that an intelligent agency had any hand in the creation of life, and for every single experiment, there must be a result predicted which would disprove the action of an intelligence.

3. Repeat step 2. A lot.

4. Publish the results obtained in a peer-reviewed scientific journal.

5. Repeat steps 2-4. A lot.

6. Sit back, relax and enjoy a beer, and keep your Nobel prize polished to a healthy shine while ID is automatically inserted into science textbooks everywhere, and becomes the new standard in science education in biology.

Do these six things and no scientist on earth will object to ID being inserted into science class. Evolution has done this many times over. That's why it's in science textbooks right now. If ID did the exact same thing, it'd be in the science texts within the next 20 years, easily.

So, who's up for it?

Thermodynamics for Creationists

Okay, so in a recent discussion, the second law of thermodynamics came up. Honestly, I can't believe that I'm having to point this out again, but the truth of the matter is that the second law of thermodynamics in no way prohibits evolution. All the second law of thermodynamics states is that the total entropy of the universe must increase over time.

So let's start with the basics. What is entropy?

The thermodynamic definition of entropy is k*ln(multiplicity)

Okay, what is multiplicity?

let' start with a simple conceptual example (which, surprisingly enough, turns out to have a real world thermodynamic version (the two state paramagnet))

Let's say you flip four coins.

How many possible ways are there for it to come up all tails? 1
How many ways are there for it to come up with exactly one heads? 4
How many ways for two heads? 6
How many ways for three heads? 4
And for all four heads? 1

Those numbers are what are called multiplicities.

Let's look at that again. Define a microstate as the specific state. ie, tails-heads-tails-tails would be one microstate. heads-tails-tails-tails would be a different microstate; but they're both part of the same macrostate (one heads). The fundamental assumption of thermodynamics is that in any given macrostate (all tails, one heads, and so on), the microstates are indistinguishable from each other. So, assuming that your coins are fair, the probability of a microstate is equal to any other.

In other words, multiplicity is effectively a measure of probability. multiplicity of some macrostate/multiplicity of all possible macrostates of a system gives the probability of that specific macrostate.

Back to our definition of entropy.

S = k*ln(multiplicity)... log is a monotonic function, so bigger it is, bigger S will be. k is boltzman's constant.

This is what entropy, essentially, truly is. The reason we say it tends to increase is because, as long as the fundumental assumption of statistical mechanics holds, higher entropy states directly correspond to higher probability states. ie, the high entropy states are literally the most likely states of reality. However, the key point here is total entropy.

Systems can easily take a entropy drop in one area so long as there's a corresponding entropy increase elsewhere. In fact, that's pretty much exactly how your refrigerator works.

First, consider if you have two systems, one with multiplicity A, the other with multiplicity B. What's the total multiplicity? A*B, right?

so therefore the two entropies would be the sum, since ln(A*B) = ln(A) + ln(B)

accept that so far?

Great. Now, let's define temperature. Temperature is not actually defined as being proportional to the energy of an object. That's a nontrivial fact about temperature. Temperature nowadays is defined thermodynamically as the reciprocal of the partial derivative of entropy with respect to energy with volume and number of particles (and external magnetic field and other such things) held constant when relevant.

Now, what does that actually mean? it means an object for which a slight change in energy would net a huge change in entropy (in the same direction) would have a low temperature, while big change in energy causing small change in entropy would have a high temperature, right? This also works backwards, if two objects, one hot one cold, both undergo a change in temperature of an equal quantity, the cold one will have a greater change in entropy than the hot one. That's pretty much the definition of the term. Again, if you're having trouble with this, I recommend you pick up a good thermodynamics text. I recommend Kittel and Kroemer's "Thermal Physics." I don't know which edition it's in now, but you should be able to find it on Amazon.

So place those two objects together. What's going happen? Well, the highest probable states are those that correspond to the highest entropy, right?

So... if energy goes from the cold object to the hot object, a lot of entropy will be lost from the cold object, while only a little entropy will be gained by the hot object. So a net decrease in entropy.

In the other direction, there'd be obviously a net increase in entropy. This is why energy goes from hot to cold. And it's a nontrivial fact, as I mentioned.

All of this is to point out the obvious: local decreases in entropy are not only possible; but they happen as a matter of routine in nature. Take crystal formation for example, or the operation of your refrigerator. All the second law of thermodynamics states is that the entropy of the universe has to go up. It doesn't matter if the entropy of a living being, or even of the entire planet earth drops, as long as there's an increase in entropy elsewhere.

Saturday, June 14, 2008

The retroviruses that are Endogenous

A blogger, SA Smith, phrased it in a way that, frankly, is hard for me to improve upon, so I'll just quote her:

If Darwin and Wallace had decided to open a resort in Cuba instead of going into science -- if every fossil were still hidden, then the second we found ERVs, common descent would have smacked us in the head like a sack full of doorknobs.

So, what are endogenous retroviruses (ERVs), and why is Ms. Smith so convinced that they are such powerful evidence in favor of common ancestry?

Let's start with the basics, shall we?

A retrovirus is pretty much what it sounds like. It's a virus that works backwards. Most viruses contain a double strand of DNA, locked within a protein coat, which is dumped into the cell. This double strand of DNA hijacks the cell's machinery and uses it to churn out more copies of itself. The DNA from the virus produces mRNA, the mRNA migrates to the cell's ribosomes and produces more proteins, and the DNA churns out more copies of itself. This is a massive oversimplification, and it doesn't apply to all DNA-based viruses, but for the purposes of this discussion, it's sufficient.

A retrovirus does this backwards. A retrovirus is a protein coat which contains single strands of RNA. Using an enzyme called Reverse transcriptase (also, pretty much, exactly what it sounds like), the RNA in the virus is reverse-transcribed into DNA which is then inserted in the genome of the cell they're attacking. That DNA then pumps out tons of copies of the virus, which then move on to infect other cells.

Now, these retroviruses have a very distinct genome of their own. As distinctive as a fingerprint, maybe even more so. In addition, they have a giant molecular flashing neon sign which says HERE IS WHERE A RETROVIRUS WAS INSERTED. Not literally. It's called the Long Terminal Repeat, or LTR, it's a specific type of sequence which has only ever been found in the genes encoded by retroviruses. Sandwiched between these two LTRs are the genes for the proteins that make up the virus. In other words, once a retrovirus has inserted itself into its host genome, it's easy to find, and the gene sequence in between those LTR signposts is easy to identify, and is so specific that a single virus can be identified within the genome.

Okay, so what?

Well, sometimes, not often, but sometimes, a retrovirus inserts itself into a germ cell, reverse-transcribes itself onto the genome of that germ cell, and becomes inactive. At this point, we call the retrovirus endogenous. This doesn't happen often, but it happens often enough that it's estimated that approximately 8% of the human genome is made up of remnants of ERVs, and because we have this giant molecular neon sign hanging on either side of them, they're pretty easy to nail down. So this ERV, newly dumped into a germ cell, gets passed from parent to child, and from that child to his or her children and so on. They get dumped into the genome at random points, but once they're there, they can stay in the genome, in pretty much the same place, for millions of years.

Every vertebrate species we've every looked at has ERVs, conserved so neatly that we can trace them back through the animal's ancestry, literally playing connect-the-dots by finding common ERVs between humans. Buried within the very molecules that make us, we have tiny molecular fossils which can be followed back millions of years.

So, let's look at the creationist viewpoint, and what this viewpoint would predict for ERVs. If all animals on earth were specially created, pretty much in their current form, then you'd expect all animals, including humans, to have completely different ERVs in completely different points of their respective genomes. In other words, we'd expect no commonality in the ERVs, either in location, or in species of ERV. If you looked at the human genome and found an ERV, then looked at the same locus in the Chimp genome, you would expect never to find the same ERV. The same applies for humans and Gorillas, and Humans and Orangutans. There should be absolutely no commonality between ERVs of different species.

However, if common descent is correct. If all animals share a common ancestor, then we should find commonalities between ERVs in a very specific, predictable pattern. Namely, animals which are more closely related should have more common ERVs than animals which are more distantly related. Humans should have a lot of ERVs in common with Chimpanzees, a few in common with other primates, and almost none at all with elephants. If we had none in common with Chimpanzees, or a lot in common with elephants, evolution (certainly the common ancestry of humans) would be disproved on the spot.

In other words, we can place these two predictions side by side and see how they match up with the available data. Is there no pattern whatsoever to ERVs in different animal species, or do we see this pattern predicted by common descent?

Well, guess what, the experiment has been done for humans and the other great apes eight years ago (Gene 2000 Apr 18;247(1-2):265-77). Sure enough, we share ERVs in common with all of the other great apes, and exactly as the theory of evolution predicts, we have more in common with chimpanzees, our closest living relative, than any of the others.

And it doesn't just work for humans. Other vertebrates have had their phylogenies worked out, and their relationship with other vertebrates and their ancestries worked. Time and time again, we can use ERVs to trace the lineage through a single species (for humans, for example, there are even a couple of ERVs which appear in some humans, but not all of them, indicating an extremely recent addition to the human genome), or between species. And that phylogeny can be laid neatly over the nested hierarchy that we've already constructed. This is easy to explain by a common ancestry. Actually, it's kinda hard to explain it any other way, but I'm willing to let the creationists try.

So by all means, what's the creationist explanation for Endogenous Retroviruses, and what evidence can you bring to bear to support that explanation?

Wednesday, May 21, 2008

Why do Creationists hate God so much?

Creationists seem to have a very low opinion of God.

From their point of view, God's an egotistical prick who requires you to believe in Her as a Conditio Sine Qua Non for salvation. She's basically a boogiewoman with a few magic tricks up Her sleeves.

Now, depending on how you define the term, I absolutely believe in God. I believe that there's a unifying governing mechanic to the universe; a binding logic, if you will; without which the universe is incomprehensible, and which may, itself, be impossible to obeserve (although I'm not ruling out that this could be measured someday). On occasion, I call that "God." I don't, however, believe in God in the Burning Bush sense of the word; and I certainly don't believe that She's the vindictive asshole that many fundamentalists seem to believe She is: vindictive and merciless enough to condemn the majority of the planet who aren't some specific religion to eternal damnation. Frankly, I fail to see how such a God deserves worship.

But for the sake of argument, let's assume that God is an intelligence of some kind. Let us postulate that there is some intellect capable of creating the universe and all life therein by a sheer force of Her will. What exactly makes the Creationists out there believe that such a being can be summarized with a select few verses of a book?

If God created everything, then Her fingerprints are upon every tree and rock. She's in every sunset and sunrise, everything living and nonliving. Her brushstrokes are in every piece of trash, every building, and every cloud. If God created everything, then the place to find Her isn't in a book; it's in the world you see when you lift your nose out of it. If God created nature, then the place to look for Her is in nature itself. That's where you're going to find God's thoughts, not in a book written by people who have been dead for two thousand years.

Postulating the existence of God, reading the Bible won't tell you what She's thinking; but looking at what She's done so far might give you some insight.

Creationists don't reveal the message God sent, they ignore it. They ignore the one textbook they can possibly know that God wrote (postulating Her existence): the universe itself; in favor of a book which has been translated, re-translated, and re-interpreted time and time again. Postulating the existence of God, they choose to ignore what She actually did, in favor of the world's longest-running game of "telephone" which may describe what She's done. They assume that God's message can be written in a few select lines of text, and won't even consider the possibility that maybe the truth is bigger than the words used to describe it. They make humanity into some kind of special creature and they make God into a two-bit deity with a couple of funky magic tricks up Her sleeves.

In fact, I would go so far as to say that scientists are much closer to having an understanding of God (postulating, of course, that She exists) than any creationist is. At the very least, those who believe in Her certainly have a far higher opinion of God than most creationists seem to. Einstein once said: "I want to know God's thoughts; the rest are details." The observant among you will realize that he never once claimed that he already knew Her thoughs. Merely that he wanted to know them. And therein lies the fundamental difference between Creationism and science. Science is humble enough to acknowledge that they don't have the answers; creationism is arrogant enough to assume that they do, based solely upon a book which She might have had a hand in writing.

Now, if we only look at the evidence for evolution, then what do we have? Postulating the existence of God, She's telling us that we're not special or more important than any other living creatures; more than that, She's telling us that we're connected to every living thing on Earth. We're connected to every tree, every plant, every microbe and virus. We're connected to every animal and insect. We're a part of each and every one of them, and they are a part of us.

Extend that a little further; bring cosmology into the mix. Now, not only are we connected to every living creature, but everything nonliving as well. We're connected to every star, every planet, every rock. We're connected to the air we breathe, the water in the streams. We're connected to every single galaxy; every nebula; every piece of trash on the ground; every blade of grass; down to the most insignificant lonely atom in deep space.

If we ignore the book for a second and look at nature, then the one conclusion that we can draw is that God (postulating Her existence) is telling us something far greater than is written in any Bible; indeed, something far greater than its authors could possibly have imagined. She's telling us that we are connected, albeit distantly, with absolutely everything.

Postulating the existence of God; what more profound and moving message could possibly be sent?

Please allow me to introduce myself...

I think it's worth explaining where I got the title for this blog. Something, historically, that scientists have not done well is making what we do cool. We're just not that good at explaining what we do to the proportion of the population that doesn't read scientific journals every day. It's hard for us to connect with the layman and explain to them why what we do is interesting, and perhaps more importantly, why it's important.

One of the great exceptions to that rule is the late, dearly missed, Carl Sagan. Sagan was one of the great popularizers of science. He had a gift to reach out to audiences of all faiths and backgrounds and talk about the wonder he felt when he looked at the universe.

One of my favorite quotes of his is this one:

How is it that hardly any major religion has looked at science and concluded, 'This is better than we thought! The Universe is much bigger than our prophets said, grander, more subtle, more elegant?' Instead they say, 'No, no, no! My god is a little god, and I want him to stay that way'

As he did so often, Sagan summarized what I have always felt about the way creationists approach the universe in one two sentences. Worse than that, creationists seem to feel that because I accept the theory of evolution I either view mankind as a worthless animal, or I view life as meaningless.

Respectfully, if people truly believe that that's what evolution says, they're full of shit.

The number of individual beings which could be standing here in your place vastly outnumber all the grains of sand, on all the beaches, in all the world. You're the inheritor of a genetic legacy which stretches back 3.8 billion years through the eons, and which has circled the center of our galaxy about 20 times. You're the endpoint of billions of generations of births, competitions, wars and deaths, the only possible sequence of hereditary combinations that can possibly result in you. Your forbears have survived arguably the single greatest ecological catastrophe ever to hit the planet, when the earliest plants started poisoning the atmosphere with oxygen. Yet, your ancestors learned to use this poisonous gas to produce energy in a way that had never been attempted before; an evolutionary triumph which paved the way for the first multicellular life. Your genetic line has survived floods, freezes and meteor impacts from the skies themselves, preserving this single genetic line through the eons to lend ultimately to you. This is a legacy you share with every living thing on earth, from the largest creature ever to have lived; the blue whale, to the lowlies prion. You share this legacy with the blades of grass between your toes and the trees that gave you shade. You are a thread in a huge, amazing, incredibly diverse tapestry of living things; some of whom have clawed their way our of the seas to survive on land, some of whom remained in the ocean and a few of whom stood on land for a few million years, ultimately said "well, screw this" and marched back into the sea. Once we add cosmology into the mix, not only does this legacy stretch to everything living, but to the non living as well. You share your origins with the stars and planets. The asteroids which hang in space, all the way down to the loneliest hydrogen atom in deep space. All the parts that make you stretch back through the eons and have borne witness to the very birth of the universe. They have seen the birth and death of stars, supernovae, black holes and pulsars. They've seen planets torn to pieces and solar systems form. They've seen galaxies coalesce and skies darken.

The universe is much more grand, more amazing, more beautiful, more elegant and more subtle than has ever been written in any holy book, and you are here, against nigh-incalculable odds to see it all. Just consider that for a moment.

If acceptance of the theory of evolution, or of cosmology, is a sign of low self-esteem, what the hell are the standards for a high one!?