The Loom

Tree Climbing

Readers were busy this weekend, posting over fifty comments to my last post about HIV. Much of the discussion was sparked by the comments of a young-Earth creationist who claims that the evolutionary tree I presented was merely an example of microevolution, which–apparently–creationists have no trouble with. This claim, which has been around for a long time, holds that God created different "kinds" of plants and animals (and viruses, I guess), and since then these kinds have undergone minor changes, but have never become another "kind."

Some readers expressed frustration that the comments were getting side-tracked into arguments about creationism. I take a pretty relaxed attitutde to what goes on in the comment threads, though. Part of that attitude, I’ll admit, comes from the fact that I don’t have the time to hover over the comments all day. But I also don’t relish the thought of shutting down discussion, except of course when comments come from pornography-peddling bots.

I myself find that objections to evolution frequently turn into good opportunities to discuss interesting scientific research. For example, let’s take the claim that an evolutionary tree of HIV merely documents microevolution.


Here’s the tree from my last post, published in The Lancet. It compares a new aggressive, resistant strain of HIV to strains taken from other patients. These viruses all descend from a common ancestor. The descendants mutated, many mutants died, and some mutants thrived, thanks to their ability to evade the immune systems of their hosts. Strains that share a closer common ancestor fall on closer branches.

This new strain belongs to a group of strains known collectively as HIV-1. What happens if you compare HIV-1 to viruses found in animals? Is it impossible to link these viruses together on a single tree? Were they all created separately, each to plague its own host? That’s what one might expect if indeed the "microevolution-yes, macro-evolution no" idea was true. After all, viruses that infect different animals are generally different from one another. They can only survive if they have biological equipment suited to their host species, and different species offer different challenges to a virus.

It turns out that the same approach used to compare HIV strains found in individual people works on this larger scale. Scientists can draw a tree.

siv tree 1.gif

Here is the most up-to-date version of the tree, which appears in the latest issue of the Journal of Virology. The different branches of HIV-1 are marked in black. The red branches are viruses known as Simian Immunodeficiency Virus (SIV) found in certain populations of chimpanzees. The blue branches also represent chimp SIV’s, but these are more distantly related to HIV-1. (A side note: the Lancet paper doesn’t specify exactly which HIV-1 group the nasty new strain belongs to. That’s a matter of ongoing research.)

It appears, then, that HIV-1 evolved into a human scourge not once but several times from chimp SIV ancestors. One likely route is the increasing trade in chimpanzee meat in western Africa. Hunters who get chimpanzee blood in their own wounds can become infected, and certain strains that manage to survive in our species can then evolve into better-adapted forms.

Of course, tracing back HIV-1 evolution this far leads to the question, where did the ancestors of HIV-1 come from? The authors of the review in Journal of Virology takes another step back, comparing chimpanzee SIV to SIVs from other monkeys. Does this enterprise now finally collapse? Does "microevolution" finally hit the wall, unable to explain "macroevolution"?

Nope. Here’s what they find. The tree on the left is based on studies of one HIV/SIV gene called Pol, and the one on the right is based on another called Env. SIVcpz refers to chimp SIV, and the other abbreviations refer to SIV’s found in various monkeys.

siv tree.gif

It turns out that different genes in chimp SIV have different evolutionary histories. This is no big surprise. Virologists have known for a long time that a single animal can get infected by two different viruses, which–on rare occassion–may combine their genetic material into a single package. The scientists hypothesize that chimp SIV evolved from SIV found in red-capped sooty mangabeys as well as SIV that infects greater spot-nosed, mustached, and mona monkeys. Just as humans hunt chimpanzees, chimpanzees hunt and eat monkeys. So they may have been infected in this manner.

You can take the same walk back in time with any virus that’s been studied carefully–or any species of animal or plant. Take us. Scientists publish evolutionary trees all the time in which they compare the DNA of individual people. They also use the same methods to demonstrate that chimpanzees are our closest living relatives, that primates descend from small shrew-like mammal ancestors, that mammals and other land vertebrates descend from fish, and so on. (I don’t have time this morning to grab examples of these trees, but if I have time tonight I will.) Certainly there are parts of these trees that are still difficult to make out. DNA sometimes evolves so much that a gene can wind up obscuring its own history, for example. But scientists have never hit the wall that creationists claim exists.


  1. #1 Daniel Newby
    March 21, 2005


    I would say they do hit a wall. Consider the DNA that codes for ribosomal RNA. The comparative genetic evidence is clear that all rRNA genes descend from a single common ancestor. No other genes are as clearly and highly conserved across all protein-synthesizing species. However the evidence is, and I choose this word deliberately, agnostic regarding just what that ancestor descended from. The snake eats its own tail.

    So far there is no fossil evidence, very little in the way of living fossils**, only the beginnings of a decent theory, and a few experiments that are suggestive. The Primordial Soupists are no better off than the Creationists, who at least have simplicity on their side. The Creationists also have the advantage of positing a falsifiable hypothesis: you can prove them wrong by mixing nonliving gunk in a flask and having living cells stochastically assemble.

    **Such as (1) viriods, naked RNA parasites that do not code for protein, (2) retroviruses, which translate from the RNA to the DNA world, and (3) various other RNA-based viruses with rather ancient genes. These do tend to suggest an ancient RNA-based way of life preceeded ribosomes, but are also consistent with RNA being a goofy and catalytically-active molecule.

  2. #2 Steve Russell
    March 21, 2005

    I think Mr. Newby is missing Carl’s point–the creationists claim that evolution has failed to produce evidence of “macroevolution”–transitions between overarching groups of animals. As with everything creationist, exactly what degree of small-scale evolution is “acceptable” to them, and what isn’t, remains vague and ill-defined, but presumably evidence of a transition from fish to fowl, from sea creature to land animal, would meet the test.

    Despite the plethora of transitional forms, the creationists continue to point to whatever “gaps” persist in the fossil record, and claim–apparently–that all the transitional forms themselves represent independent “kinds” that never evolved into each other. (The designer either “planted” them there, for mysterious reasons, or they somehow–even goofier!–represent the expression of information that has been contained in the genetic code since the “beginning,” just waiting to unfold…)

    Since the fossil record will apparently never satisfy the creationists, Carl suggests looking at the genetic record. Whether or not the history of the ultimate ancestor has been “overwritten” by subsequent evolution, the genetic record documents in great detail the common descent of mammals, birds, reptiles, and amphibians from fishy forebears. This is certainly potent evidence of “macro-evolution,” whatever vagaries of definition the creationists hope to hide behind, regardless of whether the process can be unraveled all the way to its origins.

    Of course, the creationists will simply respond that the “designer” fiddled with the code to make it look that way, because “he” wanted all the critturs to be similar enough to eat each other, or some other hokum… But there’s always the hope that some genuinely-confused individual out there may “grok” what Carl is saying.

  3. #3 Ken Shackleton
    March 21, 2005

    Carl….I read your blog every day and I must say that I find it very detailed and informative. Your arguments are compelling, but I am afraid that the Creationist [which I am definitely NOT] will still simply parrot “It is still just a virus” without any real knowledge of what they are saying.

    The fuzzy boundaries of their “kinds” will always give them a refuge to protect their ignorance.

    If they do reply with “It’s still a virus”…wouldn’t that be in much the same class as saying “It is still a metazoan” when they are given supporting evidence for the evolution of more familiar creatures?

  4. #4 Daniel Newby
    March 21, 2005

    Steve Russell said “I think Mr. Newby is missing Carl’s point–the creationists claim that evolution has failed to produce evidence of ‘macroevolution’…”

    Any “creationist” who claims that is obviously an idiot. A true believer would not presume to tell God that He could not create creatures that evolve, for His will is mysterious and beyond the ken of man. In any event the answer the macroevolution leaves unanswered the question of the origination of life.

    My point was that the fossil record has a mighty big gap between supernova-remnant and DNA-coding-for-rRNA. We have unquestionable objective science for both, and almost zero for the gap. It certainly has enough room for a little divine intervention. I’m mystified why self-appointed creationists ignore such an “embarrassing” corner of paleontology and spend all their effort contradicting basic hard science.

  5. #5 Thomas Palm
    March 22, 2005

    Newby, the current crop of creationists tend to be fundamentalists who believe that genesis is a exact description of how God created the Earth. Thus retreating to the position that God created the first organisms and let them evolve from that isn’t enough, this is still in contradiction to the bible.

    Nor is “God in the gaps” a viable theory in the long run as science has a tendency to fill in more and more gaps forcing religion into more and more obscure corners of the world. Once the Gods lived on top of the highest mountain, but as people climbed it and found none they have been forced to imagine them as more and more remote.

    Not too long ago it was believed that there was some mysterious life force in all organic matter, and it came as a surprise that organic compounds could be synthesized from inorganic. You think creationism could be disproved if only people were able to make a living organism in a test tube, but I think you underestimate the ingenuity of the creationists. They will be able to come up with excuses such as that even if life *can* evolve by chance that is not how it really happened, as the Bible clearly states that God created the species.

  6. #6 mccm
    March 22, 2005

    It strikes me that until you find a creationist that is not part of an organized religion that you haven’t got any one to have a real debate with. Religious belief is belief based on faith. Faith is recursively unshakeable, and the more evidence you place against it the more self-righteous a religious person gets to feel as they withstand this latest “test”. You ought to send them to the library not for Mayr and Lewontin, but for Camus, Kafka, Beckett, and Joyce. They made a pretty damn convincing case for me. The Castle is highly recommended. Shoot…tell’em to stop protesting and making a racket in school board meetings and just start praying that creationism is taught in schools. If they’re right about God then I’m sure what they want will be borne out. I have a prior commitment to materialism.

    BTW, has anyone here read Edward Hooper’s “The River”? It has a rather more provocative answer than chimp meat for the transfer of SIV to HIV. I’m curious whether Mr. Zimmer has read it and made a decision that chimp meat is still most likely.

  7. #7 Zhiyun Chen
    March 22, 2005

    I am more and more convinced that religiousness is genetic, based on some recent studies. There are alwyas little mystries in life that science can not explain. And some people will always atrribute to supernatural causes. Hence there is no point arguing with them. The only solution seems to be evolutional, to “displace” the religious population with enlightened one. But, sadly, guess who are having more babies?

  8. #8 Jeremy Human
    March 22, 2005

    Taking a step back, I just wish the religious would demand the same amount and quality of proof in their own beliefs that they demand of evolution. I’ve never seen such hypocrisy. It’s quite amazing.

  9. #9 Dan S.
    March 23, 2005

    Great contrast between the explanatory power and sheer hard-headed, hands-on practicality of actual science, compared to the the fuzzy-headedness of religion being forced to masquerade as science . . .

  10. #10 Michael Williams
    April 2, 2005

    I linked to this via my post titled “Evolution: Similiarity Implies Common Ancestry” but was unable to send a trackback ping.

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