Unbiased Research

By: Christopher

The problem with science is everyone is biased when conducting experiments. This is not some ground breaking point I'm making in this post - everyone knows this fact. If you're studying breast cancer, you have an idea of how breast cancer works before you even run your experiment. Then, regardless of what results you obtain, you always view them in the light of your initial bias. Or even worse, you set up your experiment with your result already in mind, and do not allow for other possibilities. The degree to which this affects science varies depending on the scientist, but it is always present. In fact there are very few experiments that are truly unbiased.

If you want to study breast cancer, you use cells from breast cancer patients for your experiments. The way science works is you use "Cell Lines," which are just cells that you can grow in the lab. So let's say if you want to study breast cancer, you use a cell line called "MDA-MB-435." That's just some annoying letters that let you and everyone else know that you are studying breast cancer.

I came across a paper last semester which uncovered decades of truly unbiased research (accidentally). The thrust of the paper was saying that MDA-MB-435 cells, which everyone believed to be breast cancer cells, were not actually breast cancer cells. Since 1982, people have been reporting findings on breast cancer that are completely false because they were using these cells.

Even though the main point of this paper was to discredit all the breast cancer research that had been done using MDA-MB-435 cells, the authors made another interesting point: MDA-MB-435 cells are actually skin cancer cells. This means that all the research done with these cells on breast cancer can now be viewed in the light of skin cancer.

What I find most interesting is now we have a vast encyclopedia of skin cancer research that is as unbiased as you can get. The researchers in no way were intending to study skin cancer when they published their results. Admittedly, the researchers still had a biased (thinking they were working with breast cancer), but a falsely based bias is almost as good as no bias. Since their experiments were not set up in the context of understanding skin cancer they did not have any preconceived notion of how skin cancer works when they planned their protocols. We can now re-examine their data and apply it to skin cancer. There will still be a bias in the interpretation of data, but the data collection is completely untainted.

If you read science papers, scientists are always trying to justify why their experiments are unbiased. Maybe the only way to do unbiased research is on accident.

Vegetarianism, or the Benefit of Following the Pack

By: Christopher

Everywhere you look, people are following the pack. Actually, that is the definition of following the pack. It just so happens that the pack is being really pretentious these days; the pack is becoming vegetarians. While there is a variety of reasons that people become vegetarians, I will just focus on one reason for the point of this post, however, the same argument can be applied to most reasons.

Many vegetarians today believe that the meat industry is detrimental to our environment. In order to protect the environment, they stop benefiting the meat industry by refusing to buy meat, and in turn become vegetarians. Many people (including myself) respond to this in disgust. Why would someone cut out an essential nutrient just to follow the pack?

Even if someone is helping the environment just to be "cool" around their friends, it is still beneficial in the long run. The obvious argument is that it does not matter if their reason is a phony one, the environment will still benefit and you should be happy. The more subtle reason is that it cultivates the phony vegetarian into a more environmentally conscious individual that will continue to be environmentally conscious later in life.

There is a story about a pilgrim that desperately wants to know what it means when the Bible says to pray incessantly. He does not understand what is truly required of him, so he finds a mentor who can help. The mentor tells him that all he needs to do is repeat "Lord Jesus Christ, have mercy on me" over and over. The mentor explains the beauty in this method; you only need to say the words. You don't even need to believe them, just move your lips and say the words. Eventually, the words become activating and something happens where it synchronizes with your heartbeat and pumps through your veins. It transforms your whole outlook, just by initially saying meaningless words.

Many religious groups follow this same practice. The Nembutsu Buddhists repeat "Namu Amida Butsu" (Praises to the Bhudda) continually until it becomes a part of their life. Likewise, the Cloud of Unknowing asks followers to repeat "God." I don't know what my Muslim friend says when she prays, but she has a string with 100 beads on it that she uses to count while she repeats a phrase 100 times.

All these religions are using the same technique that my vegetarian friends use to save the environment. If they continually do something (not eat meat) to save the environment, regardless of their true intentions or if they even care about the environment, it will eventually synchronize with their heart and pump through their veins. When they grow into an adult, they will be more environmentally conscious and maybe will even recycle.

Source: Franny and Zooey by J.D. Salinger

In Response To: "Insects, Sex, and Selection"

By: Christopher

In response to Insects, Sex, and Evolution, I would like to weigh in on the offhand statement that Chris put forth:

"Do conclusions drawn from the laboratory coincide with those drawn from the field (assuming that the field provides a more accurate depiction of reality)?"

To assume that the field provides a more accurate depiction of reality than the laboratory is a common pitfall that many scientists fall in to. The often unspoken assumption seems logical; however, it can lead to decades of setbacks in the scientific community if haphazardly assumed. The progression of X chromosome research perfectly exemplifies this point.

Human males have a single X chromosome, while females have two X chromosomes. To compensate for having an extra X chromosome, females essentially silence one of their X chromosomes early in development, leaving them with a single functioning X chromosome analogous to males. This process, entitled "X chromosome inactivation," is essential for the survival of females; if neither or both X chromosomes are mistakenly silenced in a female cell, the cell will die.

When looking at females in "the field" (females that go to the doctor to get checked out), an astonishing fact is realized: all females have a single activated X chromosome. This means that for females with a disease where they have only a single X chromosome, their single X chromosome does not get silenced. This also means that females with a disease where they have three X chromosomes, two of their X chromosomes are silenced leaving a single active X chromosome. The most astonishing cases in "the field" are females with 4, 5, or 6 X chromosomes: no matter how many X chromosomes a female in "the field" has, she will always silence all of them but one.

If you make the false assumption that what you observe in "the field" is an accurate depiction of reality, then the logical question follows: How do cells count X chromosomes? Clearly, cells must be able to know how many X chromosomes they have before they can silence all but one of them. A cell must be able to know that it has 5 X chromosomes before it can silence 4 of them. So how do cells count chromosomes?

This question has been repeatedly asked for the last twenty years, but has remained unanswered. It is an impossible question to answer, because it relies on the false assumption that "the field" is an accurate depiction of reality.

In this case, "the field" is a skewed depiction of reality; "the field" showed that cells inactivate all of their X chromosomes except for one. What scientists have neglected to realize for the last twenty years is that "the field" is only composed of individuals and cells that have survived. What scientists are now beginning to realize is that the cell likely does not have a mechanism for counting X chromosomes. Instead, in a developing female, cells with more than two X chromosomes will start silencing chromosomes at random. If, for instance, the female has 5 X chromosomes, some cells in the developing female will silence 5, while some will silence 4, 3, 2, 1, or none. Only the cells that end up silencing 4 X chromosomes will survive, and the female will develop from those properly silenced cells.

Additionally, scientists are beginning to realize that most developing females with an abnormal number of X chromosomes die before being born. Only the females that were lucky enough to randomly have the right number of X chromosomes silenced in the majority of their cells survive.

The important conclusion to be drawn from this lengthy explanation of how X chromosome inactivation works is that scientists assumed that cells must have some way to count their chromosomes because all of their "field" observations led them to this logical question. "The field", in this case, was greatly skewed though, because it only took into account living individuals and living cells. To correct for this hindrance, scientists have moved to studying X chromosome inactivation in a synthetic laboratory setting, rather than in "the field" from human samples.

Craig Venter, Synthetic Biologist

By: Christopher

Craig Venter is, without a doubt, the leading scientist alive. Due to his recent accomplishments, people even outside of the scientific community have heard of him, but they are often misinformed on his work. This is an attempt to give credit to what Venter has truly accomplished, and eradicate false ideas regarding his discoveries.

Venter's first great achievement was sequencing the human genome. Although this accomplishment is not the subject of this post, its story is relevant to understanding Craig Venter. In the 1990s, the US government was funding a 10 year study to sequence the human genome. Without going into the science, the method that was being used was slow, expensive, and inaccurate, so Venter stepped in and sequenced his own genome with a shorter timeline.

The reason Venter is going to win the Nobel prize though, is not for sequencing the first genome, but for another accomplishment, and subject of many news headlines from last summer:

"Scientist Craig Venter Creates Life for the First Time in Laboratory"

While his accomplishment is remarkable, it is often misunderstood because of inaccurate headlines such as the one shown above. Venter did not create life, or a synthetic organism, like most newspaper articles argue. Instead, Venter claims to have created a synthetic genome.

In his Science publication entitled, Creation of a Bacterial Cell Controlled by a Synthetic Genome, Venter describes his elegant protocol for synthesizing a genome. He took the known genome of a bacteria and tweaked it on a computer. Once a genome had been constructed on a computer, he devised a technique to construct a chromosome containing the genome. This construction of an artificial genome based off of a bacterial genome is Venter's true accomplishment; he synthesized a genome containing all the genes necessary for life using chemicals that anyone can purchase.

The distinction must be made though, that Venter synthesized a genome, not life. The reason he did not create life is because a genome, by itself, is not living. If you put a genome in a pool of nutrients, it will just float around and break down over time. To self-replicate, a genome needs much more than the DNA that Venter constructed. It needs proteins, lipids, and other cellular components, which Venter did not create. Instead, Venter put his genome into a cell from a living organism. This cell (although it had its original genome removed) had all of the components necessary to self-replicate and become life once Venter added his synthetic genome. Venter merely added the final component to revive a cell that was once living.

Finally, the applications of creating synthetic life are often overstated or misunderstood. Venter and others argue that we can now program bacteria to do useful things for the world (such as break down trash, produce drugs, etc). While this is true, creating a organism with a synthetic genome is an expensive project to accomplish something that we can already do. It is already very efficient and inexpensive to program bacteria to accomplish tasks for us, without creating their entire genome from scratch. Scientists currently add additional genes to bacteria that contain already functional genomes. This process has been going on for decades and is how insulin and most antibiotics are made.

Venter's accomplishment is monumental and should not be diminished just because it does not live up to the false headlines. Venter successfully created a chromosome far larger than anyone has constructed in the past. Additionally, and most importantly, he created the first genome that contains all the necessary genes for life. While this project is still decades away from creating life, it is still Nobel Prize worthy, as we will see within the next decade.