Episode #4: AIDS, Holford and Evolution 101

The fourth episode of Consilience is out! You can download the mp3 here (mp3 / 23.2mb) and the file’s page on Archive.org is here.

Teaching Angela to Appreciate History
On the 2nd of April 1984, Commander Rakesh Sharma became the first Indian in space. Sharma joined an Intercosmos Research Team aboard a Soyuz T-11 with two Soviet cosmonauts. The Indian Space Research Organisation (ISRO) is the primary body for space research under the control of the Government of India, and one of the major space research organizations in the world. In 2008, ISRO successfully launched its first lunar probe, Chandrayaan-1 which discovered water in the moon’s regolith.

Listener Feedback
Apologies about the poor sound quality. We’re working on it!

News
Mass graves in Zimabwe won’t be analyzed by any qualified scientists; instead,
“traditional African religious figures will perform rites to invoke spirits that will identify the dead.” We collectively facepalm.

Zimbabwean churches ban AIDS medications, hundreds die. What’s the harm?

AIDS deaths in South Africa are down 25%. An estimate in the Journal of Acquired Immunodeficiency Syndrome concluded not implementing a feasible ARV policy earlier cost “at least 3.8 million person-years for the period 2000-2005.” 330,000 lives lost. (A slight factual mistake crept in here. Michael said AIDS is defined as having fewer than 200 T-cells per milliliter of blood. The correct figure is fewer than 200 per microliter).

The Southern African HIV Clinicians Society and the Treatment Action Campaign wrote an open-letter to South African pharmacy chain Dischem over them promoting Patrick Holford. The CEO of Dischem responded. We’re not impressed. The Dischem ad promoting Holford’s South African tour is here.

CSIR to research plant supplements.

Separating red giants, from reallllly big red giants.

101
Our first 101 segment is about evolution.

  • Recommended books: Parasite Rex, Microcosm, and Evolution: The Triumph of an Idea by Carl Zimmer. The Selfish Gene, The Blind Watchmaker and The Ancestor’s Tale by Richard Dawkins. And Darwin’s Dangerous Idea by Daniel Dennett.
  • Recommended website: TalkOrigins.
  • Recommended podcast: Evolution 101.
  • An explanation for the evolution of the bacterial flagellum (pdf).

Announcements:
Sceptics in the Pub Joburg is, err, tonight. If you’d like more timely invites, join the South African Skeptics Facebook group.


About Michael Meadon

Michael Meadon is a graduate student in cognitive science at the University of KwaZulu Natal in Durban, South Africa. When he's not procrastinating online or propitiating his wife, he investigates the effects of rapid & unreflective facial judgments on political elections. He expects to graduate any decade now. When he was an innocent undergrad Michael studied Politics, Philosophy & Economics at the University of Cape Town. Unfortunately, he had to find out for himself that "social" and "science" often don't go so well together.
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24 Responses to Episode #4: AIDS, Holford and Evolution 101

  1. James says:

    Hi. This was a very good episode. I enjoyed it a lot.

    I think the 101 idea is well worth the effort. Your intro to evolution is informative, clear and (to me) enough for a beginner to start exploring the concepts. I now need to start looking for beginners with whom to share this.

    And don’t beat yourselves up about the “gloomy health news”. If I hadn’t heard about these items here, I probably wouldn’t have heard about them at all. It’s the first step to a proper reaction from Sceptics.

    Thanks!

  2. Nobody says:

    Firstly, if you want to sound like you aren’t recording this over a bad cell phone line, go buy one of these: http://www.samsontech.com/products/productpage.cfm?prodID=1878 It is cheap for what it does (pattern switching, allowing omni and cardioid), and the usb option means you won’t need to get a pre-amp. If your budget doesn’t allow, then at least switch to a mic on a high-end webcam. I’ve had tolerable results with this: http://www.logitech.com/en-us/webcam-communications/webcams/devices/6333 Also, turn off your damn phones.

    Now for the complaints (By singling these out, I don’t want to give the impression that everything else was ok):
    1) “Whenever you combine all four of these characteristics, you will get evolution” – Utter bollocks. An obvious counter-example: RNA viruses at stable mutation/selection equilibria. The high mutation rate continually drifts the viral population away from the optimal solution, while the selective pressure draws it towards the optimum, and a stable equilibrium occurs (see viral quasi-species for a related but distinct notion). So while there is heritable variation and selection, the gene frequency doesn’t change over time, which is how you initially defined evolution. Your (“quote unquote”) “exceedingly powerful argument” seems to implicitly assume that the variation was all present at the beginning of the scenario, and no new variation is introduced. Whenever you have mutations, you admit the possibility of the counterexample, and, whenever you don’t, the variation will tend quickly to nothing. Either way, if you want evolution to follow as some kind of logical necessity, you need to come up with a better argument.

    2) “When two cows mate, they make another cow. They never make a sheep” – Someone has been reading the creationist literature a little too much. This is actually a serious concern. You spend so much time defending evolution that you let the creationists frame most of the discussion. Just explain it properly and it will speak for itself.

    3) Neutral changes: “… as a result, the proportion of each generation that will inherit each trait will be random” – Ok, but, for finite populations, the proportion of each generation that will inherit a change is pretty much always random, even under strong selection. I’m not sure “random” means what you think it means.

    4) “Come on guys. Release a report like this. Seriously. Put the pdf of the damn thing online” – What the hell is wrong with the details here?: http://aids.actuarialsociety.org.za/ASSA2008-Model-3480.htm There are multiple explanations, and the actual model itself for you to run. ASSA go through a lot of trouble to make these models available for general use. This is extremely unfair and offensive.

    Keep up the good work.

    • We’re working on sound quality. Thanks for the suggestions.

      (1) I see your point here, but I think you vastly overstate its force and consequences. If a “high mutation rate continually drifts the viral population away from the optimal solution” then, by definition, evolution has occurred, no? Clearly, the equilibrium to which you refer is dynamically stable. So… it’s not a counterexample. (If you can find a natural population that remains exactly stable across generations, you’ll be up for a major award or two). In fact, on the definition of evolution I cited (which is the modern synthesis definition) evolution happens when (consequential) mutations happen.

      (2) “This is actually a serious concern.”? What? The possibility of cows producing sheep? Or are you disputing the fact that some traits are heritable? If not, what’s the point of this comment?

      (3) Random means just what I intend it to mean. (C.f. Paul Grice). And what I intended it to mean is entirely clear from context. I am familiar (too familiar) with the ultimately fruitless Socratic technique of intellectual warfare via definition. I am not interested.

      (4) They issued a press release about a report, but then didn’t (AFAIK) put the report online. It’s neither unfair nor offensive to suggest that that’s a silly thing to do, even if some technical details are online.

      P.s. As a rule, I don’t allow anonymous comments because it encourages trolling. If you see my reply and want to reply in turn, please identify yourself.

    • Angela says:

      Additionally, if we click on the “ASSA2008″ links, we get this:

      “Access Denied !!!

      Please login with your user details.

      If you do not have a username and password
      0R
      have forgotton your password, please contact the site owner.

      support@ukubona.co.za
      Thank you.”

      If you have access, perhaps you could send us a copy? That would help a lot.

  3. Robert says:

    Hi Angela,

    You need to click “Register Here” and create an account to download any of the actual models. This is entirely standard, and lets the developers know how many people are using the software. Unless you are actually running the model, you will probably just want the pdfs at the bottom, and I don’t think you need to login for this.

    Michael, that press release is about the model itself, and the results from SA data. Besides the details on that page, I’m not sure there is anything else for them to post online. They really aren’t withholding anything.

    1) ” “high mutation rate continually drifts the viral population away from the optimal solution” then, by definition, evolution has occurred, no? ”

    No? Indeed. You neglected the second bit: “selective pressure draws it towards the optimum”. Some individuals move away, and some towards. So the expectation of the frequencies of future generations remains constant. Dynamic stability is irrelevant, because the gene frequency of the whole population is stationary (even though “movement” within the population occurs) so, by your definition, the population is not evolving.

    “(If you can find a natural population that remains exactly stable across generations, you’ll be up for a major award or two). In fact, on the definition of evolution I cited (which is the modern synthesis definition) evolution happens when (consequential) mutations happen.”

    (Note, in advance, that I’m not disagreeing with your conclusion. Evolution occurs. I just don’t think your argument that supposedly makes it a logical necessity works.) Obviously for any non-homogenous finite population, genotype frequencies are unlikely to be the same across generations. If you are resorting to that, then your “exceedingly powerful argument” reduces to “inheritance is random so gene frequencies change”. If that is the case, then what were those four conditions all about? Also, if your argument works, then it should work as the population size tends to infinity, and stochastic effects disappear. This is important, because many important models of evolution work with infinite population sizes.

    “I think you vastly overstate its force and consequences”

    If your argument actually worked, it would make a number of interesting situations impossible. Please don’t teach people wrong.

    2) Please read my original point again. The last two sentences. This is obviously just a preference and recommendation. Please consider it.

    3) It was indeed clear what you meant, but that use of the term leads to confusion when reading the actual literature. If this is meant to be educational, then you should be leading people in the right direction.

    So my first post was a little angry. The ASSA thing really pissed me off. You came across as incredibly pompous and judgmental, when it really was your own inability to google. If I were you I would cringe to think of Rob Dorrington and co hearing that.

    • Thanks for your reply.

      I am really quite baffled by your anger about ASSA. Saying “c’mon, put the report online” (even if we’re wrong) is neither pompous nor judgmental. It certainly wasn’t meant to be a ringing condemnation, it was simply a quick aside.

      • Robert says:

        Listen to the section again. Pay attention to your tone. Anyone who (God forbid) trusted your assessment would get a negative impression of ASSA, when really they are being perfectly decent about releasing their stuff.

        You’re seriously telling me this doesn’t make you die a little inside? It should.

        I take it you now agree with me on the other points?

      • Owen Swart says:

        Robert I think you’re reading too much into our “tone”. It’s an entirely subjective matter, and far too open to bias introduced by your own, preconceived notions.

        If we actually made a factual error or not is another matter, but basing a claim on your perception of our tone of voice isn’t exactly a firm grounding.

      • Robert says:

        Hi Owen,

        Your tone is fine. I’m guessing a poll about Michael’s would agree with me, however. If Michael is going to be pompous, at least help him be right. And help him admit when he is obviously wrong. He appears to lack that ability.

      • Robert says:

        Also, Owen, I’m curious about your claim that (I can’t recall the exact wording) chimps are as genetically differentiated from the common ancestor (of humans and chimps), as humans are. This implies equal rates of evolution, which shouldn’t necessarily be our default expectation.

    • Angela says:

      I will be more thorough in the future.
      What I was trying to communicate is that this should be easier to access, all of the economic reports I access for my day job provide a short version which is freely available at the click of a button. If I see that I have to contact an administrator, in my experience, it normally means there is either a pay-wall or a complicated registration process.

      Please let us know of any future errors, but maybe count to ten first? That way you won’t come off as being such an aggressive bully.

  4. I have listened to it again. No it doesn’t.

    Nope.

  5. Robert says:

    Point out where I’m wrong then?

    • I think you’re right that scarcity, inheritance, variation and time don’t necessarily lead to evolution because it is just possible for drift and selection to be in balance, keeping gene frequencies in a population exactly stable. I’m wondering: do you know of any populations (natural or lab-reared) that exhibit no changes in gene frequencies at all? If there are such populations (I have my doubts, but I suppose there could be) then it’s certainly something we’d have to correct on the show. Something that is a mathematical possibility but doesn’t actually ever occur, much less so.

      I’m honestly still not hearing it, but I’ll also be sure to say nice things about ASSA in case anyone else was rendered sad by my tone.

      • Robert says:

        “I think you’re right that scarcity, inheritance, variation and time don’t necessarily lead to evolution because it is just possible for drift and selection to be in balance, keeping gene frequencies in a population exactly stable.”

        Good. Are you at all interested in attempting to fix your argument? If you ever use it again without appropriate caveats, you’ll be no better than a creationist.

        “I’m wondering: do you know of any populations (natural or lab-reared) that exhibit no changes in gene frequencies at all?”

        Assuming you mean genetically heterogenous populations, do you mean (a) populations that exhibit no changes in the frequency of any genes? Or (b) just populations where one gene is heterogeneous but with stable frequencies? If (a), then we won’t have data, because we don’t routinely do full genome sequencing of large populations. If (b), then I guess I could look around. When you say “no change”, what tolerance are you comfortable with, and over how much time or how many generations?

        Whatever you might mean, the existence of real-life examples is irrelevant when refuting an “in-principle” argument: an in-principle counterexample suffices. You retracted, and now the disagreement is one of emphasis, which is often not worth fighting about. But this is the internet…

        So, coming up with actual examples would be one way to convince you that your argument is not just wrong, but importantly wrong. There are others. I could list some important scenarios that your argument would disallow. This would also give you cases to test your revised argument against.

        1) Already mentioned: mutation selection equilibrium. I’m happy to grant that this is might only be important for understanding RNA viruses where mutations rates can be higher than fixation rates. That said, it is *very* important for understanding RNA viruses, and concepts like viral quasispecies.

        2) Equilibrium caused by frequency dependent selection. Note that this could be dodged by requiring the “variation” condition to entail differential fitness. At equilibrium, differential fitness disappears, along with the counterexample.

        3) Balancing selection caused by heterozygote advantage. This is a bit of a killer. It is an extremely important phenomenon but rendered impossible if your argument is correct.

        There are most likely others, but I’ve got actual work to get back to. Convinced yet?

  6. Pingback: Episode #5: Danie Krugel, banning reflexology and Carl Zimmer | Consilience

  7. “Are you at all interested in attempting to fix your argument?”

    How about: scarcity, inheritance, variation and time will almost always result in evolution? The conditions under which gene frequencies do not fluctuate at all from generation to generation seem to me to be extraordinarily unlikely. On the order of a flipped coin landing on its side. Of course, defending this argument thus is a kind of pedantism – the existence of dynamically stable populations bears this out.

    • Robert says:

      Facepalm.

      Then: “Certain variations will be better at surviving than others… the proportion of organisms with those strong teeth will be higher than before”.

      Now: “The conditions under which gene frequencies do not fluctuate at all from generation to generation seem to me to be extraordinarily unlikely.”

      Do you see how you have now moved the goalposts? Your argument initially attempted to show that there would be a systematic increase in variants with higher fitness. For the kinds of examples I’m providing, this is entirely wrong. Sure, in real-world finite populations, there may be some wobble around the equilibrium, but that wouldn’t be allowed by your initial argument which concluded with a systematic – if stochastic – increase in beneficial gene frequency. As I’ve already asked, if you’re happy to rely on the wobble, then why don’t you just rephrase your argument as “populations are finite therefore evolution”? You’re clearly trying to conclude something stronger, but failing.

  8. Paul Giess says:

    Just dropping in to say I am enjoying the podcast. Downloaded them and listened up to the first half of this one so far this weekend. Sound quality has been poor yes but you are right the content is still worth it. I’m sure it will get better and episode 4 already sounds far better. You’ll look back on the first few episodes and laugh somewhere around the 200th I guess.

  9. Basil says:

    Hey folk.

    Good work, keep it coming.

    We had (might still have) sound issues the links do work and we might use them on our show.

    @ Robert… what is more important:

    a. Celebrating the fact that there are voices in the world that advocate the use of science and it’s method and propose to send that message out to others that are less aware of the technicalities involved…

    or

    b. Being right at all costs?

    Thank you for the link on the samson microphone btw.

    People are listening and learning folk, well done and keep it coming.
    :)

    • Angela says:

      Thank you for the encouragement Basil.
      The sound issues should be improving (although we are now down to one laptop to record on so everybody is sharing a microphone), hopefully we will be able to invest in some recording equipment in the next few months.

      This is a massive learning experience for everyone involved!

      -AM

    • Robert says:

      Hi Basil,

      “@ Robert… what is more important:
      a. blah celebrating blah…
      or
      b. Being right at all costs?”

      All costs? Did I kill someone? Blow something up? No. I tried to engage them in rational argument – the very thing they claim to value. I find it quite amusing that Michael claims to be a skeptic when he is totally incapable of revising his position even when it is so painfully obvious that he is wrong.

      I’ll celebrate when they produce something worth celebrating. Do you honestly think these podcasts are so captivating that anyone who is anti-science will actually listen to them? Voluntarily? And if their intended audience is already scientifically literate, then ffs please make sure you don’t teach them wrong.

      Glad the mic link helped. Please only speak truths into it.

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