Image via Wikipedia

The semester is over, and I can now share some of my assignments. Usually, I try to write posts that are written with the blog in mind, in a more conversational language, less uptight, and more.. well, flowing.

This time, however, I thought it will be interesting to share this essay with you, as it was an exercise in critical thinking, one that I enjoyed researching. It raises some important issues about the scientific method and how important it is for scientists to constantly make sure they follow it.

I hope this essay gets you thinking. It sure as heck got me!

Note

This was written as an essay for World Civilization 101 class at City College of New York, Fall 2009.

The purpose of this essay is to examine the methodology used during the discovery and publishing of the Lucy bones, as an exercise in critical thinking. Nothing more, nothing less.

The Essay

In 1972, at the Hadar Formation in Ethiopia, Donald Johanson’s research team discovered the skeleton of a young biped creature they named “Lucy”. This creature showcased humanity’s evolutionary transition from quadruped apes to biped humans before the development of intelligence – a revolutionary idea for its time. Johanson’s methodology, however, had some significant flaws. It is bad scientific practice to start research with the desired conclusion in mind, since that can lead to bias towards fitting the evidence to the desired conclusion rather than examining and analyzing the available evidence objectively.

The search for human ancestry has been ongoing for the past century since the publication of Charles Darwin’s “Origins of the Species”. As more evidence comes to light about the ‘branches’ of the evolutionary tree, researchers are able to form better hypotheses about humans’ ancestors. This is a vast scientific endeavor, involving researchers from a variety of fields from Evolutionary Biology to Paleontology. As pieces of the puzzle are revealed, so grows our knowledge about the history of life on our planet.

In 1972, a group of researchers led by Donald Johanson, founding director of the “Institute of Human Origins” of Arizona State University, set out to discover a hypothesized human ancestor in the Hadar Formation in Ethiopia. Johanson’s group hypothesized the existence of a biped human ancestor, with the ability to walk upright like humans, while having a relatively small cranial capacity like that of an ape. This creature, Johanson hypothesized, would be a “missing link” between the apes and humans, and prove that humans developed the ability to walk upright before developing higher intelligence, which was opposed to the common belief at the time.

Much like in matters of State, separation of responsibilities is crucial to the process of an objective scientific investigation. In Johanson’s team’s case, the team shared the three basic responsibilities of the preliminary research: collecting the data, interpreting and analyzing the find, and formulating a conclusion. This was a mistake that will continue to influence their methodology. To make matters worse, the research group came to Ethiopia with a clear hypothesis already in mind, and their method of analysis followed their conclusion rather than vice versa. This methodology is flawed because it allows for the possibility of confirmation bias and selective data. The process of gathering evidence is already subjective, as it depends on both what the researcher is looking for and what he deems relevant. When the search is biased, the results are bound to be biased as well.

The first step in the group’s research procedure was looking for bones that could be of interest. The search and scan for bones is subjective. While in the process of gathering bones, the gatherer scans the ground for items that might be of interest. This criterion, however, is set by the collector himself, who is looking for evidence that fits his hypothesis. Theoretically, the researchers could have encountered a piece of bone that does not fit his hypothesis and therefore not have collected it, assuming it to be irrelevant.

Johanson’s first discovery consisted of a few pieces of a knee bone. At first, Johanson thought the knee to belong to a monkey or baboon, but it didn’t seem like it belonged to such an animal¹. He sent the bones to Owen Lovejoy, an anatomist and part-time forensic expert. Lovejoy examined the bone fragments and concluded that they appeared human; the joint could “lock”, suggesting the animal could walk upright. This was an important discovery showing an ancient bipedal creature. If the bones’ age was consistent with Johanson’s hypothesized “missing link”, it would serve as supporting evidence to Johanson’s theory.

There is no way of dating the bones directly. Instead, the paleontologists dated the layers of volcanic ash above the bones. They reasoned that the layer of ash above the bones accumulated after the bones fossilized². Therefore, if the ash could be dated, the bones would most likely be at least the age of the layer of volcanic ash above them. However, this assumption is problematic. The area where the bones were found is a flat expanse, known to be subjected to the power of the elements, namely flash-floods and winds. Such phenomena can easily disturb and shift the different layers of dust and ash from one place to another, rendering this dating method unreliable.

Johanson’s agreement with the Ethiopian government meant that he could not take any bone away from the field unless he proves them to be of significance. As a result, Johanson wanted his evidence to fit his hypothesis. The vast majority of found evidence was eventually substantiated by external analysis, but some remains questionable, and the method itself allows for the possibility of confirmation bias and subjectivity that only serves to undermine the validity of Johanson’s final conclusion.

Lucy’s entire skeleton was found about two and a half kilometers from the site in which the bipedal knee joint was found³. The conclusion that both fossils originate from the same species is questionable, and might have been influenced by Johanson’s pre-existing biases. To this day the argument continues about the validity of the dating of Lucy’s bones, as well as the other scattered bones found in the same vicinity. This argument does not add credibility to the claim that the knee joint Johanson found previously belongs to the same species as Lucy, or even that they are from the same period of time.

As was mentioned before, dating the bones relies on dating the surrounding ash, a method that can lead to erroneous conclusions due to natural phenomena that could shift the position of the bones and the ash. This possibility of error increases even further when a large amount of scattered bones is dated. If the dating is erroneous, and the individual bones do not belong to the same period of time, then the conclusion of them being of the same species is even more questionable. While the general estimate regarding their age is probably true, the date range is still large enough to allow the possible deviations in dating to mean a large difference in speciation. Johanson’s conclusion that the scattered bones are of the same period – and therefore belong to the same species – needs further corroboration.

When Lucy’s bones were examined, they didn’t add up to her being a biped. The pelvis was the biggest problem, as it didn’t seem to allow for Lucy to walk upright. Johanson and his team declared it misshapen and decided to begin a reconstruction. The reconstructed pelvis was found to confirm the hypothesis. Again, the team responsible for the reconstruction is not an external, 3rd party objective team, but rather the same team that operated with the same pre-established hypotheses in mind. There is no way of avoiding biased reconstruction – or biased analysis – when the same team performs both procedures.

Under examination, Owen Lovejoy, the team’s anatomy expert, hypothesized that the bone crushed and fossilized misshapen, causing the position of the bones to seem as if they “flared up like a chimp’s.”⁴ This initial conclusion might have been the correct one, but Lovejoy was part of Johanson’s team, and as such, his analysis was done under Johanson’s influence. Johanson concluded that this chimp-like bone was an illusion, and the reconstruction that followed resulted in a bipedal pelvis. It is unclear how certain the researchers can be that the final result was the original shape of the bone, but one thing is clear – the reconstruction was done under the influence of the initial and final conclusion. When the assembly and analysis of the bones are done by a team of researchers already pre-disposed to a specific hypothesis, it is little wonder that the evidence ends up fitting the hypothesis.

Lucy’s bones were found semi scattered in “Locality 162”. Next to this location, in a site later named “Site 333”, thirteen more skeletons were found and titled “The First Family”⁵. All thirteen individuals’ bones were scattered at the same relative location, which led Johanson to hypothesize that they all died at the same time, likely from a natural occurrence like a flash flood. He reasoned that they all belonged to the same species. However, this conclusion is questionable. By itself, the location cannot necessarily attest to the bones actual age, for the reasons discussed above. Further, to this day various groups of researchers are in disagreement about the species that the “First Family” belongs to, and even to the idea that they all belong to the same species⁶). The hypothesis that the creatures were all killed together by a flash flood is largely discounted, based on other geological evidence⁷. An alternate theory states that the individuals were brought over to the field by a group of predators, likely large cats, a theory that can explain the lack of certain types of bones that are suspiciously missing from the scattered fossil field. If this is true, the “family” of bones might not belong to the same species at all, as it seems the predators carried different individuals from all over the area.

Johanson didn’t just seek to prove his hypothesis with his own discoveries, but tried to apply the findings of other researchers as well. In 1976, around the time Johanson’s team discovered “Lucy”, a team led by Mary Leakey conducted similar excavations in a remote part of Tanzania. Leakey’s team discovered mysterious foot prints embedded in the ground, covered by volcanic ash. The footprints showed the distinct shape of a biped creature, almost indistinguishable from the footprint of a modern human. This discovery was incredibly significant, as the ash above these footprints was dated to be 3.6 million years old – much older than the known human ancestors at the time⁸. However, Johanson used this discovery to support his own theory, claiming the footprints belonged to the same species his team found in Ethiopia. Not only was there no corroboration to such claim, there was no reason to assume such a correlation at all, as the two sites were hundreds of miles apart.

The only immediately obvious correlating factor between these fossils is the fact they were discovered around the same time. But the discovery date has no bearing on the age or nature of the fossils discovered. Today, researchers believe the footprint wasn’t made by Australopithecus Afarensis (“Lucy’s” species) but rather belong to Australopithecus Africanus, a completely different species. Johanson’s hasty conclusion that his and Leakeys finds are correlated was done out of a desire to prove his conclusion rather than properly weighing the evidence, further allowing his initial bias to affect his final determination.

Johanson came to Ethiopia meaning to find a “missing link” in the evolutionary ladder – a term that is today no longer used by the scientific community. Of course, just like in a physical ladder, finding an extra link between previously existing ones only proves to produce two more “missing links” – before and after the newly found one. Beyond this problem of semantics, this creates an additional problem where the researchers are severely influenced by their own hypotheses and bias. The research team begins with a hypothetical conclusion about the species to be found and that place the species “takes” in the evolutionary ladder, and continues to fit the evidence to this hypothesis. This frame of mind can obscure some of the likely explanations, one of which is that the species found is not necessarily a direct ancestor for human beings, but rather exists in a parallel branch in the “tree” of evolution.

Johanson performed his analysis with his hypothesis in mind. His conclusion that the bones shared Lucy’s species was influenced by this presupposed hypothesis, and the risk for confirmation bias could not be negated. Today, the scientific community still argues some of Johanson’s findings, a fact that serves to demonstrate the problems in his scientific methodology.

Bibliography

• BBC h2g2. The Laetoli Footprints. 17 February 2003. 17 October 2009 <http://www.bbc.co.uk/dna/h2g2/A944336>.
• Donald C. Johanson, Maitland Armstrong Edey. Lucy: The Beginnings of Humankind. Simon and Schuster, 1990.
• Heslip, Steven. Australopithecus afarensis. 2001. 21 September 2009 <https://www.msu.edu/~heslipst/contents/ANP440/afarensis.htm>.
• “In Search of Human Origins.” Nova, PBS, 3 June 1997.
• Kreger, C. David. Australopithecus afarensis. 20 September 2009 <http://www.archaeologyinfo.com/species.htm>.
• Wikipedia. AL 333. 26 September 2009 <http://en.wikipedia.org/wiki/AL_333>.
• —. Laetoli. 17 October 2009 <http://en.wikipedia.org/wiki/Laetoli#The_footprints>.
• —. Lucy (Australopithecus). 26 September 2009 <http://en.wikipedia.org/wiki/Lucy_%28Australopithecus%29>.

Footnotes

1. “In Search of Human Origins.” Nova, PBS, 3 June 1997. http://www.pbs.org/wgbh/nova/transcripts/2106hum1.html
2. “We can’t date fossils directly, but we can date the ash. And once we know how old the ash is, we know that any fossil found beneath it is at least that old.” Don Johanson, “In Search of Human Origins.” Nova, PBS, 3 June 1997. http://www.pbs.org/wgbh/nova/transcripts/2106hum1.html
3. “In Search of Human Origins.” Nova, PBS, 3 June 1997. http://www.pbs.org/wgbh/nova/transcripts/2106hum1.html
4. “In Search of Human Origins.” Nova, PBS, 3 June 1997. http://www.pbs.org/wgbh/nova/transcripts/2106hum1.html
5. Wikipedia. AL 333. 26 September 2009 <http://en.wikipedia.org/wiki/AL_333>
6. Gordon, A. D. (2007). Strong postcranial size dimorphism in Australopithecus afarensis: Results from two new resampling methods for multivariate data sets with missing data. American Journal of Physical Anthropology, 311-328. (Taken from Wikipedia
7. Johanson, D. (Winter, 2004). Lucy, thirty years later: an expanded view of Australopithecus afarensis. Journal of Anthropological Research, 60(4), 472., Reference taken from Wikipedia, AL 333, “Cause of Death” section.
8. Wikipedia. Laetoli. 17 October 2009 <http://en.wikipedia.org/wiki/Laetoli#The_footprints>.

There is one little piece of us, though, that holds the secret to our existence, and the history of our species: The DNA.

My main interest is usually physics and astronomy, but I have always been fascinated by that double-helix molecule and its meaning, both philosophically and realistically; since the beginning of Genetics the human race have progressed exponentially. It’s just, simply, amazing.

So when the “rogues” of “The Skeptic’s Guide to the Universe” Podcast debated the history of DNA discoveries, I decided it is time for some biology experiment.

I am about to show you how to extract your own DNA from your own bodies in your own kitchen. Yourselves.

It’s aliiiiiiiiiive!

The Experiment

This experiment allows you to extract DNA matter from cells from your mouth, and is very similar to what Friedrich Miescher discovered. His discovery was from pus, and this one is from your mouth. Physiology can be funny like that.

What do you need?

For this experiment,you will need the following tools:

• Two beakers.
• A glass or a cup. You can use one from the previous experiment.
• Liquid soap (NOT antibacterial. You shouldn’t use those at all anyways).
• 2 test tubes or clean and clear bottles. I used “travel-size”empty plastic bottles for the experiment. These work, just make sure they are properly cleaned with distilled water.
• Distilled water.
• Rubbing Alcohol.
• Sodium Chloride. Well, Salt.
  Sodium Chloride is a nice and fancy way of saying “Salt”. You don’t need anything other than table salt, or cooking salt, but for fun, I suggest going to your nearest pharmacy and try to ask for a small amount of Sodium Chloride.
  I did, and the nice lady replied it is a prescription drug. Worth the chuckling, I promise.
• Glass rod (I used wood, because I didn’t have glass, but wood isn’t as good at all.. try to get a glass rod).
• Anything that can be used to measure the liquids. The more accurate your solutions are formed, the better your results would be.
• Drinking water. Preferably bottled water, to avoid varying amounts of chloride or other contaminants.

The Process

You can find the process I used for this experiment in the repository of About.com biology expert, but here’s a short summary:

1. Solution #1 (Negative-charge Ions to bond the DNA molecules together): 8% Sodium Chloride + 92% Distilled Water.
2. Solution #2 (Breaking apart the cell membranes and “freeing” the DNA from the nucleus): 25% Liquid Soap + 75% Distilled Water.
3. Wash your mouth thoroughly; you want DNA from the cells in your cheek and not from whatever animal (or fruit) you ate for lunch. Make sure your mouth is CLEAN.
4. Swirl about 10ml of water in your mouth. Use the bottled water and NOT the distilled water! If you want a larger amount of cells, do it a bit ’stronger’. Do that for about 30 seconds.
5. Spit the water into the cup. You have just gathered a bit of cells from your own body, congratulations.
6. Take 1ml of Solution #1 (Sodium Chloride) and add it into an empty, clean bottle (or test tube).
7. Add the cell-water mix you just spit out into the same bottle (or test tube).
8. Add 1ml of Solution #2 (Liquid Soap) into the same bottle (or test tube).
9. Close the cap or seal with a test tube stopper.
10. Twirl, swirl, and turn the bottle upside down and right side up gently. Do not shake. You’re not 007.
11. Add 5ml of Rubbing Alcohol into the bottle while tilting it slightly so the alcohol ends up floating on top of your mixed solutions.
12. Wait for about 5 minutes.
13. Watch. If you want, you can do what I did and move the DNA strand from the solution bottle to a clear bottle that contains alcohol only. I keep my little creation next to my computer screen.
    Make sure you do it very gently.

What’s happening?

Well, DNA exists inside the nucleus of a cell. So to see it, you need to first let it out of its confinement. But that isn’t enough – DNA molecules are positive charge, so they reject one another. In order to see the strand, we need to make sure a bunch of these molecules bond together. Finally, DNA melts in water but not in alcohol – we will use that to “trap” the strand so we can look at it.

So, here’s the summary:

1. Soap has detergent in it, that dissolves the membranes (the “skin” of the cell) and releases the DNA from the nucleus.
2. Sodium Chloride is negatively charged, so it bonds the DNA strands together to create a long strand we can see in the naked eye.
   Correction:
   Okay, I got this wrong again, so ailboles was kind enough to explain it and give links, too!:DNA is a negatively charged molecule. It is the positive ions (in the Sodium Chloride solution) that interact with the DNA (see http://ppge.ucdavis.edu/Equipment/Protocols/thymus_dna_extraction_03.pdf under the section, “Answers to Student Activity” number 5)
   
   Well, that makes more sense. Thanks again to ailboles for taking the time and effort to explain this again!
3. Alcohol “traps” the strand, because it doesn’t break apart in alcohol, only in water.

There you have it. Your own DNA in a bottle. Beats wooden boats any day.

About Scientific Discoveries

Usually, when we hear that someone a long long time ago made a very big discovery we tend to be skeptical. It’s understandable – I find it hard to see anyone getting along without a fast-paced computer, let alone working without an electron microscope, or a light bulb.

But the truth is, usually scientific discoveries don’t just “pop up” miraculously. We tend to remember the people who invented specific “gizmos”, or wrote a patent relating to a specific discovery (like Edison and the Light bulb, Bell’s telephone, and Morse’s telegraph), but they were rarely “the first”. The research started a long time before, and their discoveries were possible only due to past discoveries.

The same is true to DNA.

The 1869 Discovery

In 1962, James D. Watson, Francis Crick and Maurice Wilkins recieved the Nobel Prize for the discovery of the structure of DNA and its hereditary role. Because the Nobel Prize is a famous honor, we tend to remember them specifically, but their discovery was possible because of many prior researches, the first of which was done by a Swiss researcher called Friedrich Miescher in 1869.

Miescher researched the human cells, specifically white blood cells, by taking blood-stained bandages from a nearby hostpital. He noticed a microscopic substance inside the pus on the bandages – and identified the substance as coming from within a cell’s nucleus. He called this substance “Nuclein”.

The following dates mark the time line that lead to the famous discovery of the DNA structure in the 1950s:

• 1869 - Friedrich Miescher identifies a substance that came out of a cell’s nucleus and has a weak acidic properties. He calls it “Nuclein“.
• 1919 - Phoebus Levene identifies the base, sugar and phosphate nucleotide units. He suggests that DNA is made of strings of nucleotide units that are connected together through phosphate groups.
• 1928 – Frederick Griffith combined “smooth” and “rough” forms of Pneumococcus bacteria, showing that DNA plays a role in passing genetic information.
• 1937 - William Astbury produces an X-Ray diffraction pattern that shows DNA has a regular structure.
• 1943 – Oswald Avery, Colin MacLeod and Maclyn McCarty identify DNA as the transforming principle – showing that bacteria transfers genetic information through a process called “Transformation”.
• 1952 – Alfred Hershey and Martha Chase confirmed the heredity trait of DNA in an experiment.
• 1953 - The structure of DNA is suggested by James D. Watson and Francis Crick, based on X-Ray Diffraction images taken by Rosalind Franklin. This is the structure that is accepted today.
• 1957 - Crick lays out the “Central Dogma” of molecular biology, including RNA, DNA and proteins, and the relationships between them.
• 1963 - Watson, Crick and Wilkins receive the Nobel Prize in Physiology or Medicine.

Practical Applications

Wow. That’s going to be a huge huge list. The discovery of Genes, structure of DNA and Genetics in general has led to countless advancements in medicine and technology. From discovering diseases earlier to devising vaccines. The list is just too great, too big, and too important to summarize in a single post. If you look at the resources, however, you could find many places to start.

• Forensic Medicine.
• Interpol’s Attempt – DNA Profiling.
• The study of Human evolution (many more resources, including this one from National Geographic, and Berkley’s “DNA, the Language of Evolution“).

Resources:

• The Experiment Instructions can be found here: http://biology.about.com/c/ht/00/07/How_Extract_DNA_Human0962932481.htm
• Extracting DNA From Fruit:
  • http://www.funsci.com/fun3_en/dna/dna.htm
  • http://www.csiro.au/resources/ps1tp.html
• Great Clip about DNA Structure: http://www.youtube.com/watch?v=qy8dk5iS1f0
• Friedrich Miescher: http://en.wikipedia.org/wiki/Friedrich_Miescher
• Albrecht Kossel: http://en.wikipedia.org/wiki/Albrecht_Kossel
• History of Electricity Discoveries: http://www.code-electrical.com/historyofelectricity.html
• Griffith’s Experiment: http://en.wikipedia.org/wiki/Griffith%27s_experiment
• Hershey-Chase Experiment: http://en.wikipedia.org/wiki/Hershey-Chase_experiment