Tuesday, January 6, 2015

On The Origin of Genieology

The Selfish Genie: "I've got this."
What your daddy and mommy were taught about genetics, like most oldskool mommy and daddy skoolin', is wrong.

Don't feel bad, Charles Darwin knew nothing of genes, yet said he knew all about how we got here.

He had a lot of genies to help, though.

But now, the age of conflating genies with genes is over, however, the new genetic reality is not yet catching on well enough.

So, today we will review the difference between the understanding during "early genetics" (The Eugenics Review Vols. 1 to 60; 1909 to 1968) with the current state of affairs for understanding genetics (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10).

Once upon a selfish gene ("The Selfish Gene" age) in a discipline long ago, genes
Feeling exceptional?
were thought to be genies in the sense of being able to draw the map of your everything.

Determinism (genetic essentialism) on steroids, as it were, taking you along for the virtual magic carpet ride.

Everyone was unique with an "isn't that special" set of genies down under the hood, genies that were like Jack's magic beans, which took you and everyone else up, up, up, rapturously along their own special, unique Highway 61, to selfish gene heaven.

That is, if you had a special gene maker genie who was selfish enough, but if not, well then it's Eugenics for you.

Then came the Human Genome Project, those damn scientists, who wrecked the daydream with this:
More problematic is the reality that the human genome is still a vast catalogue of the unknown and scarcely known. The Human Genome Project’s most startling finding was that human genes, as currently defined, make up less than 2 percent of all the DNA on the genome, and that the total number of genes is relatively small. Scientists had predicted there might be 80,000 to 140,000 human genes, but the current tally is fewer than 25,000 — as one scientific paper put it, somewhere between that of a chicken and a grape. The remaining 98 percent of our DNA, once dismissed as “junk DNA,” is now taken more seriously. Researchers have focused on introns, in the gaps between the coding segments of genes, which may play a crucial role in regulating gene expression, by switching them on and off in response to environmental stimuli.
(One Man's Junk Gene Is Another Man's Treasure Gene?). What do you mean ... human genes fit somewhere between "a chicken and a grape" (What's Eating Gilbert Grape?).

Then, along came two real insults to our trek up the stairway the genie had promised.

The first was that we are really buggy, that is, we have more bacterial and viral (microbe) genes than we have "human" genes:
... some 90 percent of the protein-encoding cells in our body are microbes ... 99 percent of the functional genes in the body are microbial ... exchanging messages with genes inside human cells ... microbes cohabitating our body outnumber human cells by a factor of 10, making us actually “superorganisms” that use our own genetic repertoire as well as those of our microbial symbionts ... We just happen to look human because our human cells are much larger than bacterial cells ... no matter how you look at it, it’s high time we acknowledge that part of being human is being microbial ...

Microbes may indeed be subtly changing our brain early on — and for what purposes we cannot yet say ... the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity ... these findings call for a complete re-examination of human physiology and immunology. Attributes that were assumed to be human traits have been shown to result from human–microbe interactions.

Some would say that genomics has been able to distil some humility into humankind. The finalised version of the human genome deprived us of the illusion that we are one of the most complex creatures on Earth — an illusion that was at the basis of some guesses that Homo sapiens was expected to have at least 100,000 genes. When we look at a table of genomes by species, and specifically at the number of genes that have been counted or estimated for each species, we notice that humans are surpassed by several plants and invertebrates.
(The Human Microbiome Congress). Now we're pissed: first we find our gene count is somewhere between a chicken and a grape, and next we find out that several plants and spineless wormy things have more genes than we do!

To top it off, our genetic make-up is not even guaranteed to be unique to us, or to be the same during our entire lifetime:
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.
(The "It's In Your Genes" Myth - 2). "Ghastly to say the least" you may be thinking, but buckle up buckaroo, I am not finished with this episode just yet.

To really genie down our Earth destroying egos, let me finish this post with the knowledge that our genes are not even alive, no, they are molecular machines:
... DNA is chemical compound ... DNA is non-living, because it is a molecule not an organism ... DNA is not living. It is a chemical - a large fragile molecule ... there is no debate in the biological community about this ...

We are involved in a project to incorporate innovative assessments within a reform-based large-lecture biochemistry course for nonmajors. We not only assessed misconceptions but purposefully
DNA molecule is not alive
changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of deoxyribonucleic acid (DNA) along with understanding in what ways classroom discussions/activities influence student conceptions. Data sources included pre-/post-assessments, semi-structured interviews, and student work on exams/assessments. We found that students held misconceptions about the chemical nature of DNA, with 63% of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA. However, the post-assessment exposed that 40% of students still held misconceptions about DNA, indicating the persistent nature of this misconception. Implications for teaching and learning are discussed.
(Putting A Face On Machine Mutation - 4, cf. On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10). Yes, those human genes that fit somewhere between "a chicken and a grape" are not even alive.

Hint for Dawkins: neither machines nor genes are selfish, even if genies are:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(The Uncertain Gene - 3, cf. The New Paradigm: The Physical Universe Is Mostly Machine). Well, well, we don't have to get out the pitchforks and go genie hunting, we still have our denial to fall back on!

Fall back to the genieology (cf. "genetic essentialism --the idea that our genes carry our fundamental essence", here, here, and here)!

More about genieology to come in future posts (so we can all know the difference between genealogy and genieology).

The next post in this series is here.

Various experts on human genetics (the first speaker in the video is Dr. Robert Morris Sapolsky, Professor at Stanford University); (cf. epigenetics)


  1. That one link points out "Almost paradoxically, the better we understand genomes, the more genetic identity becomes a social construct rather than a scientific fact." (link)

  2. In the next episode of this series ("On The Origin of Genieology - 2"), I will take a look at the revolutionary study "Forget the selfish gene — the evolution of life is driven by the selfish ribosome" in the context of the Dredd Blog hypothesis "The Cosmic Robosome" which was set forth in "On the Origin of the Genes of Viruses - 5" and "On the Origin of the Genes of Viruses - 6" (both were mentioned in this current post).