Bias in Science

An illustration of the differences between RNA and DNA
(click for credit and a larger image)

Several years ago, Dr. Ivan Oransky (MD) and Adam Marcus (MA in science writing) started a blog called Retraction Watch, which reports on scientific papers that have been retracted by the journals that published them or the authors who wrote them. It provides a valuable service to those of us who frequently read the scientific literature, because many journals and authors don’t promote their retractions nearly as much as they promote their papers. Thus, if I want to see whether or not an important publication in the scientific literature has withstood the scrutiny of other scientists, I can check this blog.

Last week, while scanning the new entries, I ran across an interesting one. It reported on a major paper published last year in the journal Nature Chemistry. Despite the fact that it was published only 18 months ago, it has already been cited by 26 other papers in the scientific literature. Why? Because it appeared to solve a very serious problem in what is probably the most popular origin-of-life scenario.

Because the origin-of-life scenario I was taught as fact at university has fallen out of favor among origin-of-life researchers, other scenarios are being explored. One such scenario is the “RNA world” hypothesis. In this view, life was not initially based on DNA. Instead, it was based on a similar molecule, RNA (the differences between the two molecules are shown in the graphic above). This view has garnered a lot of attention, because RNA can do something DNA cannot. It can speed up chemical reactions without being used up in the process.

Why is this important? Many chemical reactions that occur in living systems happen slowly on their own. To be used by a cell, they need to be sped up. Cells do that today with enzymes, and they make those enzymes based on instructions that are found in their DNA. The problem is, of course, that a living system is needed to replicate DNA. But that living system depends on the information stored in DNA. How was DNA originally produced if its very replication is based on the information it contains? The RNA world gets rid of that problem.

Because RNA is very similar to DNA, it can store the genetic information a cell needs to be alive. However, some forms of RNA can also speed up chemical reactions without being used up. In the “RNA world,” then, the first cells carried their information in RNA, and they also used RNA to speed up their chemical reactions. Enzymes and DNA then came later, as these simple living systems began to evolve.

One of the many problems with this origin-of-life scenario is that in all studies so far, RNA needs enzymes in order to replicate properly. Other RNA molecules could, in theory, do the jobs that enzymes are doing now, but no mechanism by which this happens has been found. That’s where the retracted paper comes in. It reports on a series of experiments that seemed to demonstrate a possible way in which RNA could be replicated over and over again without the help of enzymes. However, when another member of the research team (Tivoli Olsen) couldn’t reproduce the results reported in the paper, the team stepped forward to retract it.

What’s interesting is an admission made by the research team’s leader, Nobel Laureate Dr. Jack W. Szostak. He said:

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

This happens a lot in science. Scientists aren’t unbiased investigators who don’t have any stake in the outcome of their experiments. Generally, when we do experiments, we are looking for some result. If we aren’t careful, that can make us see things which aren’t really there. In this case, that’s what happened to the authors of the paper.

Now don’t get me wrong. I am not writing about this to insult Dr. Szostak and his team. In fact, I applaud them! Not only did they step up and do the right thing (regardless of the consequences), but Dr. Szostak even freely admitted the reason for the error. I am also not saying that because of this retraction, the “RNA world” hypothesis is wrong. I think it is, but not because of this retraction. Those who really believe that living systems can form as a result of random chemical reactions should continue to investigate the “RNA world” hypothesis, even though I don’t think they will find enough evidence to indicate that it’s a viable mechanism.

I am writing this so that people understand there is no such thing as an unbiased scientist. We all approach science with our inherent biases, and those biases affect our results. The problem isn’t the bias. The problem is that so many scientists (as well as science journalists and science educators) pretend that it doesn’t exist!

18 Comments

  1. John D. says:

    pfffft. People accused me of being biased when I was trying to force that ape jaw into my homo sapien skull. Well I certainly turned the tables on them when I said “We don’t know what the tools of evolution were.. they certainly could have been hammers, drills, sandpaper and 2-part epoxy!”

    1. Alaska Nivanuatu says:

      Haha, do you have that on video, John?

      1. John D. says:

        Sorry Alaska, Museums and research institutions have limited funds and if I give away my secrets then I won’t be able to sell these suckers any more. ; )

        1. Alaska Nivanuatu says:

          if you sold them on ebay, maybe I’d bid on one. I could use it as a prop while quoting Shakespear xD

  2. Alaska Nivanuatu says:

    That’s interesting, I was just reading about this a couple days ago: https://evolutionnews.org/2017/12/prominent-retraction-vindicates-meyer-and-signature-in-the-cell/

    The interesting point they made in this article is that Dr. Jack W. Szostak, before pulling the paper and admitting that his research team was ‘blinded by belief’, had commented regarding ID: “I think that belief systems based on faith are inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.”

    Also that the retraction vindicates what Steven Meyer wrote in Signiture of the Cell: “I began to reflect on the failure of these simulations to explain the DNA enigma apart from the guidance of intelligent scientists. I wondered if they hadn’t inadvertently provided evidence for a radically different approach to the problem of biological information. This led me back to where I had started — to the idea of intelligent design and to a consideration of the scientific case in its favor.”

    Thanks for blogging on this! What I appreciate about what you wrote is the point you make, that scientists can be biased, and it’s okay to acknowledge that scientists can be biased.

    I hope that more scientists (evolutionists, creationists and IDers alike) follow Dr. Szostak’s fine example and admit when they’re wrong and/or biased.

  3. Mathew Irwin says:

    Dr Wile, thanks for this. We have been reading more about ID lately…and picked up some books by Dr Meyer…we have known for some time that no one is absolutely impartial. That would be a miracle wouldn’t it? Understanding what one’s worldview is actually part of the exercise!

  4. Bill McClymonds says:

    I thought John and Alaska might like this short video. It gets interesting about the 1:58 mark. I think he meant power grinder rather than saw.

    https://www.youtube.com/watch?v=EeO0JlZsXio

    1. Alaska Nivanuatu says:

      Oh yeah, I remember that. Still hilarious! Thanks Bill!

      What I want to know is, were Dr. Owen Lovejoy’s methods ever questioned by the mainstream scientific community?

      1. Christopher says:

        I’m no expert, but my understanding of that video is that he was following standard fossil reconstruction procedures, and that the original bone placement really was anatomically impossible.

        1. Alaska Nivanuatu says:

          I’m no expert either, but if he was following standard fossil reconstruction procedures, it seems he should have used more finesse. Instead, he appears to be carelessly hacking away chunks of plaster with a power grinder. The original bone placement at least appeared much more anatomically probable than the hacked plaster pieces.

          If the concern was that pieces has broken off or degraded after the deer (or something) has stepped on them then it seems that the reponsible thing to do would have been to create plaster molds and then ADD ON more plaster instead of grinding plaster off.

          And if there was a need to do fossil reconstruction, then why didn’t they do it when Lucy was discovered, back in 1974, or soon after? 20 years seems like a long wait to me.

          Again, I’m no expert either. These are just observations from a layman that could be completely off. It’s possible it took that long to discover the need for reconstruction, and he could be following correct reconstruction procedures. But it’s also possible that Dr. Lovejoy was “blinded by bias” and recreated Lucy’s hipbone just to look more like a human’s.

      2. Christopher says:

        I think the pieces did fit together more elegantly when reconstructed, but I would suggest that for the sake of the documentary, it was shown occurring in a more crude manner (such as the way he “shows off” his new reconstruction with nothing actually holding it together) in order to give the audience a sense of discovery, almost as if they were right alongside Dr. Lovejoy, discovering the answer to the puzzle in real time, which was not actually the case.

        In another paper, Dr. Lovejoy wrote in a figure caption: “While much of the iliac blade is well preserved, the posterior third has been crushed, crumpled, and bent anterolaterally almost exactly 90o (PSIS: posterior superior iliac spine). Since the dis- lodged portion includes the auricular surface, the anatomical structure and relations of the pelvis cannot be determined prior to restoration; indeed, if the sacrum and unrestored innominate are articulated and mirror-imaged, a gap of several centimeters occurs at the pubic symphysis. Therefore, analyses of the hip joint of A. afarensis that are based upon its unrestored condition must be disregarded in discussions of its locomotor behavior.”

        That would seem to explain his reasoning behind the idea that it was anatomically impossible. I cannot say how true or untrue his statement is, as this is vastly out of my field of expertise, but it does make some sense to me.

        As to the question of why it took 20 years to make this discovery, it would appear that it did not. Upon further research into this matter, I found reference for the reconstruction in 1979:
        Lovejoy, C.O. (1979). A reconstruction of the pelvis of AL 288 (Hadar formation, Ethiopia). Am. J. Phys. Anthrop. 50, 460.

        I am unable to read the actual publication without paying for it and thus cannot confirm when exactly the reconstruction occurred, but there are multiple published papers (including those written by Dr. Lovejoy) which use the paper in question as a citation concerning the pelvis and bipedalism, thereby adding plausibility to the completion of reconstruction occurring sometime near 1979.

        I should note that I did find reference to another study suggesting that any bipedalism in these creatures were not the same as bipedalism in humans.
        As long as Dr. Wile has no problem with me posting links in the comments section, the study I mention is found here: http://www.sciencedirect.com/science/article/pii/S0047248484710165

        1. Alaska Nivanuatu says:

          Thank you Cristopher, that’s very helpful.

          Yes, you’re right, the reconstruction took place in 1979. I’d just assumed the reconstruction took place on the same year the documentary was made (1994).

  5. Bill McClymonds says:

    I had some thoughts based on the comments made by Alaska and Christopher. First, it is my understanding that the bones in both the hands and feet of other A. afarensis, when present, are significantly curved. Those bones weren’t present in Lucy. In my opinion, a primate with curved bones in the feet is always arboreal and would have a flared pelvis.

    Second, there is a huge amount of prestige, fame and often monetary reward for finding new or different human ancestor remains. The people who find these remains have a tremendous incentive to reconstruct the remains in a way that brings them the most fame or income.

    Third, Dr. Menton was an anatomy instructor. I think he could reasonably infer the proper anatomical reconstruction based on what he observed. Differences from human anatomy would have been easily distinguished by him.

    Fourth, the clip I posted was only a part of the full video. I will link the full video below.

    https://answersingenesis.org/media/video/evolution/lucy-shes-no-lady/

    Fifth, all of the naturalist attempts to show human or other natural evolution are simply rabbit trails to me. The naturalist must first explain how a process with absolutely no intelligence was able to produce the brilliance of the DNA code very rapidly from a naturalist point of view. Dr. Wile has posted information about synthetic organic chemist Dr. James Tour previously. Dr. Tour has challenged anyone to show him how to go from simple chemicals to the necessary amino acids, proteins, etc. that are the building blocks of life. According to Dr. Tour, no one has even come close at this point. To additionally explain how the coded information of DNA arose from conditions of zero initial intelligence seems absurdly improbable to me.

    I know someone might try to give an explanation like the RNA world hypothesis or some other theory. That person should first go talk with Dr. Tour. He will even buy them lunch … at least according to his You Tube video presentation that I watched.

    1. Alaska Nivanuatu says:

      Thanks Bill, I’ll watch the full video when I get the chance.

      I think the case for Lucy being fully (or at least nearly fully) arboreal is pretty clear cut, thanks to the work done by Christine Berge (see link in Christopher’s comment) and Evolutionists Brian Richmond and David Strait:

      “In addition to wrists designed for knuckle-walking, Richmond and Strait noted that Lucy also had neck, shoulder, arm, finger, and toe anatomy suited to arboreal life.” (https://answersingenesis.org/human-evolution/lucy/a-look-at-lucys-legacy/)

      However, while I think it’s possible (indeed, even probable) that Dr. Lovejoy recreated Lucy’s hipbone to look more human and achieve “prestige, fame and monetary reward” (and he certainly did achieve these things) I don’t think it’s ever fair to assign motives to anyone for any reason (especial since many people unfairly assign motives to creation scientists). Just because he “could have” doesn’t necessarily mean he “did.”
      One could just as easily say that Dr. Menton critized Lucy’s pelvis reconstruction in order to gain prestige and fame in creationist circles.

      I’ll also point out that you are using the argument from authority when you say “I think (Dr. Menton) could reasonably infer the proper anatomical reconstruction based on what he observed,” although you’re probably correct.

      One thing I’m wondering, though is this: did Dr. Menton ever critize Dr. Lovejoy for Lucy’s pelvis reconstruction before the PBS Nova documentary in 1994? He had 15 years to do so.

      Here’s an interesting (and very biased) article that discusses this:
      (https://northstatescience.wordpress.com/2011/01/01/correcting-creationists-redux-was-lucy’s-pelvis-reconstruction-a-fraud/)

  6. Bill McClymonds says:

    Thanks for the comments Alaska. I want you to know that this reply is done with gentleness and respect. My first point was to strongly suggest that Dr. Menton had good cause …and video evidence … to say Dr. Lovejoy had not accurately reconstructed the pelvis. You seem to agree on that point.

    My second point was a general comment. It was intended to apply to anyone involved with the discovery of possible human ancestor remains. It was not intended to be directed at any one particular individual.

    As far as an argument from authority is concerned, I thought it might not be obvious to everyone reading the comments on this post that Dr. Menton was an anatomy instructor at one time. He was not an entomologist commenting on anatomy. Some degree of authority is necessary when challenging another person who has a reasonable degree of authority in the same general field.

    I read the article you linked prior to making my comments. I agree with you when you say it is very biased.

  7. Alaska Nivanuatu says:

    Thanks for clarifying your intentions, Bill, I really did think you made some very good points, but I also enjoy playing devils advocate.

    I did watch the full video, and I really enjoyed it. Dr. Menton presented some great evidence and concern regarding Lucy’s skull, hands, feet, and knee structure, among other things.

    What I really would have liked to see, though, was more detailed discussion on WHY Dr. Lovejoy’s pelvis reconstruction was (or was not) inadequate. In that portion of the video, there is much more pointing and laughing rather than critical examination, which bothered me, and I think it opened Dr. Menton up to a lot of attack from critics.

    If you or anyone else knows where I can find a critical examination on how Dr. Lovejoy’s pelvis reconstruction could have been inadequate, I’d really like to see it.

    I did find this article in science direct that describes a new reconstruction of Lucy’s pelvis done with computed tomography and three-dimensional modeling techniques: (http://www.sciencedirect.com/science/article/pii/S0047248409002176)

  8. Bill McClymonds says:

    I don’t have full access to the article you linked Alaska, so I can’t adequately comment on it from just an abstract. If you want some speculation on the Lovejoy reconstruction, I can give you an opinion. It may not be accurate, so take it for what it is worth. I am open to correction by anyone who is more familiar with what actually took place.

    In the video, Dr. Lovejoy says the fracture has caused the bones to fit together so well that they are in an anatomically impossible position. I had to think about that statement for a while. I think what he is saying is that the bones are in an anatomically impossible position for upright bipedal locomotion … like a human walking. If I am correct in my understanding of what he is saying, I would have to agree with him.

    I think what he is trying to explain is that there has been a compression fracture at the sacroiliac area. I think he is saying the ileum was compressed into the sacrum by the force of the damage that was done to it. That compression fracture then caused the pelvis to rotate into a position that was not natural for the individual and made it appear more like a chimpanzee pelvis. The explanation in the video was that a deer possibly stepped on the pelvis at some point in time, although pre or post fossilization is not explained.

    My problem with the explanation is that the supposed compression fracture created a “perfect fit”. In my opinion, a deer stepping on the bones wouldn’t apply adequate force to create a compression fracture that would fit perfectly. I think the amount of force adequate for compression and rotation with perfect alignment would have been more likely to shatter the specimen into hundreds of pieces if it was fossilized at the time of the traumatic event. I have a considerable amount of difficulty imagining an event that would have both compressed and rotated the iliac alignment to the sacrum without pulverizing and destroying much of the specimen.

    Once again, this is only speculation based on my understanding of what I think Dr. Lovejoy was trying to communicate. If my assumptions are correct, Dr. Lovejoy’s proposed solution is difficult for me to accept based on what I think would be an extremely low probability event. A compression fracture of the type I think he is trying to suggest seems ludicrously improbable in my opinion. Since he then went on to reconstruct the pelvis based on his hypothesis, his reconstruction was significantly flawed because of his flawed presuppositions.