biology

What if our family tree was still around?

Sometimes I wonder what our world would be like if our evolutionary relatives were still around. How would things be different with intelligent cousins like Neanderthals in the mix? Would we just be perpetually trying to kill them off, since that’s probably what helped them originally go extinct? Would there be nations of Neanderthals or would we intermix? Would their be stigma with interbreeding (which we know sometimes happened) or general species-ist stereotypes? Would there still be tension from the genocide we inflicted on them ages ago, with reparations to current Neanderthals or monuments to those who lost their lives?

Would less intelligent cousins who still had primitive language, like Homo heidelbergensis, be relegated to a lower class? How would we treat our even more distant cousins like Austrolopithecus? Would we grant them some special rights above other animals, like we sometimes do with intelligent animals like dolphins and chimpanzees? How would the ethics of genetic testing work when trying to get samples from our cousins who are not intelligent enough to consent, but are still more intelligent that what we currently research?

…This is what a human evolution researcher with a penchant for science fiction daydreams about. I guess I’ll add it to the list of “Books I should write but probably never will.”

Nazis, genetically modified babies, Mothman, and Jesus

I didn’t think those topics could be combined, but I’ve been proven wrong. No, it’s not the next hit superhero movie. One of the “perks” of being an atheist blogger is that I get signed up to all sorts of wacky mailing lists for creationists, woo peddlers, and conspiracy theorists. I suspect they think this annoys me, when really it usually goes straight to my spam folder to die with all the penis enlargement ads. But sometimes things slip through to my inbox, and sometimes their insanity is hilarious.

I present for your entertainment, “V Blast: THE BEAST REVEALS THEY CREATED GENETICALLY MODIFIED BABIES”

Those who are aware that conspiratorial practices have already wildly exceeded even the most fantastic speculations were not surprised to hear that scientists have now admitted that genetically modified babies have already been born. Although the mainstream, or the so called “ethical” medical community is now publicly acknowledging they’ve mixed genes from multiple parties to produce designer babies all the way back to the late 1990’s, the reality is genetically engineered babies were probably born as far back the 1940’s in one of Joseph Mengele’s Nazi laboratories.
Generally speaking, secretive “black” science significantly precedes the allegedly legitimate version, in which the mainstream commonly lags behind by decades. In fact, the recent mainstream media exposure in the Daily Mail periodical, reignited interest in a subject which was actually covered, albeit rather quietly, years earlier.
It turns out that In Vitro Fertilization (IVF) clinics have been using a technique now for years that “rejuvenates” the eggs of women who are having trouble conceiving, by injecting components of another woman’s egg. This component is called cytoplasm, and it contains the mitochondrial DNA from the donor – thus making the resultant baby the product of 3 parents – the father, and two mothers.
It turns out this has been publicly known since 2001 and, by tracing the research (and the scientist who developed the technique), we learn that babies with more than 2 parents were born at least as far back as 1997. Once again, once such things go public, it virtually always means it’s been going on for quite a bit longer, and has gone much further than is generally acknowledged.
Time for a science break! It’s actually true that scientists are trying to develop methods that use a third individual’s mitochondria during IVF, but it’s not to make abominations or super babies. It’s to cure diseases caused by malfunctioning mitochondria. Mitochondria are the “powerhouse” of the cell, making lots of energy so your cells can actually function.
They also have their own genomes because they were once a separate organism! They were engulfed by another type of cell and the two formed a symbiotic relationship, and now every eukaryote (anything that’s not bacteria or archaea) has mitochondria. Mitochondria are passed from mother to child, not father to child. This is because egg cells have the room to store mitochondria, but sperm don’t.
So if you have a disease that’s caused by a mutation in the mitochondrial genome, you could technically suck out all the “defective” mitochondria and replace them with “healthy” mitochondria from another person. And people are going nuts at the ethics around this, because yes, technically you’d have a third genetic “parent.” If you want to learn more, read this great article in The Guardian.
For instance, there is nothing to indicate these maniacs have stopped at 3 parents, as they could have, theoretically, added the cytoplasm of a dozen women – each selected for what are perceived as desirable characteristics – i.e. blue eyes from mom #4, physical speed and agility from gymnast mom #5, a very high IQ from mom #6, and so forth.
Yeah, theoretically you could add all sorts of mitochondria. But mitochondrial genomes are tiny and don’t really contribute to any distinguishing traits. Things like eye color would still be determined by nuclear DNA (the ones egg and sperm contribute to).
To put it another way, this is the stuff the Nephilim were made of.
I’m not even going to touch that.
What happens if they try to splice in the mitochondria of another father is anyone’s guess, but such outcomes could look like something out of a horror film. And it gets worse.
Actually, nothing different would happen if you took the mitochondria from a man. The only reason mitochondria are transfered maternally is because eggs have the room to do so. There are rare examples of mitochondria being transmitted paternally, with no real consequences.
Now we’ve learned the key research embryologist who pioneered this technique left the fertility clinic work he was doing, and was hired by a US military medical institution. This chilling fact begs the question, is there anyone who seriously doubts the military establishment will seek to engineer a super-soldier, and will not be deterred by any of those messy moral or ethical considerations?
Christian Media, the ministry which fields the V Channel output such as the V Blast Internet letter, the Eclipse printed periodical, and the Exotica TV and radio show, has previously produced material on the efforts to create robo-soldier. In what looks like a Marvel Comics fiction, hardly anyone knows military scientists have already succeeded in growing (with spider DNA) a dense, Kevlar like compound, directly into the skin of solders, so they can withstand a bullet wound (see the Exotica TV episode on the subject).
Military scientists are talking about using spider silk to make structures that are stronger than Kevlar…but they can hardly hardly make enough with the current technology, and they definitely haven’t started breeding genetically modified soldiers. We don’t have that technology. We hardly understand how spider silk production works.
With such efforts, one can only wonder if these madmen will eventually produce a modern version of the mothman, replete with wings that can quietly transport the organic killing machine behind enemy lines. Furthermore, it is certain the Biblical prophets described just what is occurring.
Oddly this was probably the paragraph that offended my brain cells the most. Mothman? Not…you know, Spiderman? I…I just don’t understand why they wouldn’t go with the obvious if they were going to invoke genetically modified superheroes.
For instance, the prophet Joel described military men that were unstoppable in very scary terms:
 “a great people and a strong: there hath not been ever the like…A fire devoureth before them; and behind them a flame burneth…and nothing shall escape them. The appearance of them is as the appearance of horses [centaurs]; and as horsemen, so shall they run. “They shall run like mighty men; they shall climb the wall like men of war; they shall march every one on his way, and they shall not break their ranks: Neither shall one thrust another; they shall walk every one in his path: and when they fall upon the sword, they shall not be wounded” (Joel 2:2-8)
For those unfamiliar with the prophetic texts, the manipulation of genetics is a primary theme found in the numerous descriptions of the end of the age. Jesus Christ said the last generation would be “…as it was in the days of Noah, so shall it be also in the days of the Son of man” (Luke 17:26)
The primary description of the days of Noah was focused on what is sometimes called the “first incursion,” wherein the fallen angels tampered with the genetics of men and women, and the offspring became “mighty men” – a population which was quickly catapulted into leadership within the old world order.
The book of Genesis tells us the whole world was “corrupt” and the LORD saw nothing but “violence” everywhere, so He purposed to destroy the world (Genesis Chapter 6). This is what Jesus used as a template for the last generation – a time of massive destruction, preceded by violence and genetic manipulation.
When coupled with the descriptions of world war, famine, and pestilence, to say nothing of the massive fraud of the so called pre-tribulation “rapture” in which millions of deceived believers “know not” that they are about to be “taken away” to the grave in a violent judgment (Matthew 24:39),  this tribulational devastation could occur at any moment.
— James Lloyd
Jesus blah blah blah.

The only other thing worth highlighting is their unique instruction on how to remove yourself from their mailing list:

Of course, if you have been convinced Christians should never send an Email to someone without permission (Did the Disciples of Jesus ask people for permission to tell them the Good News?), then we will cheerfully delete your name from our database.

Woah, gettin’ a little defensive there. Of course I want to stay subscribed! I love getting a good laugh at conspiracy theorists with no solid grasp of science.

The tale of Taq

One donor requested that I talk a little bit about polymerase chain reaction, or PCR.

PCR is now a super common laboratory technique for people doing any sort of molecular biology. It’s a way of amplifying a specific section of DNA so it’s present in millions of copies. This is really important if you want to, for example, sequence a specific gene. You want that gene to be present in such high quantity compared to the rest of the genome so nothing else is sequenced.

As for how it works…I’m not sure if I’m able to explain that in a coherent way right now, so here’s a handy dandy video!

Most PCR uses a specific type of DNA polymerase known as Taq. Taq is an enzyme that was originally isolated from Thermus aquaticus, a thermophillic bacteria that lives in hot springs and hydrothermal vents. Taq is special because it can withstand high temperatures without losing its function. Since PCR requires DNA polymerase to be functional at higher temperatures, this makes Taq super important. The one downside to Taq is that it’s not very good at proofreading, which makes it error prone. Thankfully DNA polymerase has been isolated from other thermophillic species. Pfu is an example of a thermophillic DNA polymerase with proofreading ability.

This is post 45 of 49 of Blogathon. Donate to the Secular Student Alliance here.

Microbiology haikus

Commenter VeritasKnight requested a post full of haikus; Joe McKen asked for them to be microbiology themed.

Peptidoglycan
damn you, I am positive
You blue my cover

It was chilling there
Before genomes went mainstream
The retrovirus

S. cerevisiae
The brewer, not the screwer
Fuck C. albicans

Ten percent human
The rest, essential strangers
Am I really me?

And for those who are curious, the themes (in order) are gram staining, endogenous retroviruses, baker’s yeast versus the species that causes vaginal yeast infections, and the human microbiome.

This is post 34 of 49 of Blogathon. Donate to the Secular Student Alliance here.

How important will genomics be for future healthcare?

Short answer: Not very.

Biologists are stuck in an unfortunate situation. Most major funding sources in the US come through the government, and it’s essential to stress the impact your research will have on humans. Basic research for the sake of understanding the unknown just isn’t enough to secure funding nowadays. Everything has to be spun to make it appealing to humans since taxpayers are the ones funding the research, and the research needs to seem “justified” in their eyes. Want to study primate microRNAs to study how primates evolved? You better mention how microRNAs are involved in cancer, even if you have no interest in studying that. Want to figure out how spider silk proteins evolved to fulfill different biological tasks? Better mention how spider silk is stronger than Kevlar even though it’s practically impossible to mass produce.

The same is true for human genomics. When the human genome project was first announced, scientists made endless promises about how sequencing the human would lead to immense advances in human health. They had to say that to get funding for this basic research project. Years have passed and we’ve learned a great deal about the human genome, but we still haven’t had the medical revolution we were promised.

Frankly, we probably never will. For most people, getting their genome sequenced is going to be a novelty. You’ll be able to learn about your ancestry, but that’s about it. Sure, you may learn you have a 10% increase in your chance of getting heart disease, but is something that small going to change your diet and exercise routine? Only a tiny fraction of people will have diseases with very high penetrance (likelihood of showing the trait if you have the gene) that can be identified by genomics. And of those diseases, few are going to have preventative treatment or cures.

And right now that knowledge is only available to the very rich, who are more likely to have better preventative health care anyway. Yes, prices of genome sequencing are dropping rapidly, but we’re eons away from every person on the planet being able the afford their genome. Even if they could afford it, it’s not really worth it. The health of people around the world would most improve by increasing exercise and by having clean water and healthy food available. I mean, diarrhea is one of the leading causes of death in developing nations…are they really going to benefit from knowing their exact risk for diabetes? There are more basic problems that we need to fix first.

The field of human genomics is still incredibly important to study in order to learn more about our species and about disease…but it’s not going to be the panacea scientists had to promise in order to receive funding.

(I should add this isn’t just a personal opinion of mine, but one that is frequently voiced by a number of professors and other scientists during various panels I’ve attended)

This is post 23 of 49 of Blogathon. Donate to the Secular Student Alliance here.

Today in traumatizing wildlife videos…

Nature is often weird. But sometimes, it’s REALLY fucking weird. I give you the pearlfish:

For those of you who can’t watch the video (though if you can, you really should)… Adult pearlfish are long skinny fish that live in open habitats. In order to not get eaten, they need to find a suitable place to hide. The problem is, they tend to live in places that are missing the typical hiding places like rocks and corals. They are, however, surrounded by lots of large sea cucumbers…so they hide by swimming up a sea cucumber’s butt and living inside of it. Most don’t harm their hosts, but some are parasitic, nibbling away at the sea cucumber’s gonads for nourishment.

This is post 14 of 49 of Blogathon. Donate to the Secular Student Alliance here.

My research part 4: How did microRNA convergently evolve?

How could microRNA have evolved to have such similar structure and function in plants and animals after evolving independently? You must be thinking, “What are the odds?!”

If evolution boiled down to nothing but random chance, the odds seem staggering indeed. No, I’m not about to say God guided evolution. What happens is there are certain traits about the system that constrain it to act in a certain way, making similar outcomes more likely.

To understand more fully, I have to teach you a little bit about microRNA biogenesis. Awww yeeeaaah!

Adapted from Berezikov 2011

In animals, a microRNA gene is transcribed to make what’s called “primary microRNA.” This pri-microRNA forms a hairpin structure – that is, it folds over and complementarily base-pairs to itself, forming a step and loop. This pri-microRNA is trimmed by the protein Drosha and is then shipped out of the nucleus as an ~80 nucleotide precursor microRNA. In the cytoplasm, the protein Dicer cleaves the pre-microRNA to form the mature ~22 nucleotide microRNA, which will go on to be involved in gene regulation.

In plants, pri-microRNA still forms hairpins, but their size can be far more variable. Plants also lack Drosha – all of the processing is done by a Dicer homologue.

You’re probably thinking, “So they’re processed differently. This doesn’t really convince me of the odds.” But what’s important to notice is that both of these systems share a couple of key things, which make convergent evolution more likely:

  1. Both use the protein Dicer to process mature microRNA. This is thought to be an exaptation – where a trait initially evolved to have one function, but has subsequently come to have another. Dicer is thought to initially be used to cleave foreign RNA particles, for example from viruses. There’s also evidence that suggests Dicer plays a role in repairing double stranded breaks in DNA. Since Dicer was already present in plants and animals because of these more ancestral functions, it was available in both lineages to be used for something else. Plants and animals didn’t have to evolve a totally new protein to process microRNA – they used the machinery they already had sitting around.
  2. Both process microRNA from hairpins. RNA hairpins spontaneously occur all the time, and some of these spontaneous hairpins give rise to new microRNA. That’s because if a hairpin happens to process into a mature microRNA that conveys a fitness advantage to an organism, natural selection will act to perpetuate it. If a hairpin results in an unfavorable outcome like disease, purifying selection will purge it from the population. Because RNA hairpins spontaneously occur and Dicer was already around, natural selection would act favorably on a system where processing hairpins leads to a fitness benefit.
I have only one thing left to say:

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My research part 3: MicroRNA in plants

Since my research focuses on primates, I don’t exactly work with plant microRNAs. But they’re still fascinating enough that I wanted to touch on them. Plant and animal microRNAs are very similar – they’re approximately 22 nucleotides in length, they’re processed from larger hairpin structures, and they function by downregulating messenger RNA. But they have a number of differences because microRNA in plants and animals evolved independently.

Yes, this similar system arose separately in the plant and animal kingdoms. No, this is not proof for God. This is an example of convergent evolution, where the same trait is acquired independently in different lineages. Think of the ability to fly in insects, birds, and bats. The evolution of microRNA is the same, it’s just more molecular instead of having an obvious effect like flight, which is visible to the naked eye.

Why do we think plant and animal microRNA evolved independently? One major piece of evidence is that there are no homologous microRNAs between plants and animals (homologous meaning shared through a common ancestor). This is especially striking when you compare it to microRNAs within animals, a number of which are homologous. There are some animal microRNAs present throughout the whole animal kingdom, from sponge to fruit fly to orangutan, that just don’t exist in plants. Plants have their own set.

Another thing supporting independent evolution is that plants and animals have different processes for generating mature microRNA. In plants, microRNA is fully matured in the nucleus before being shipped out to the cytoplasm for use. In animals, much of the processing takes place out in the cytoplasm. Animals have additional proteins that are involved in processing – I’ll touch on it a little more in my next post. Also, plant and animal microRNA differs in how it targets messenger RNA. In plants, the whole ~22 nucleotide microRNA is involved in complementary base-pairing with the messenger RNA. In animals, only a 7 nucleotide “seed region” of the ~22 nucleotide mature sequence determines which messenger RNA it’s supposed to match up with.

A final piece of evidence is that microRNAs are missing in other forms of life. They’re absent in fungi, placozoans (the most basal animal lineage), and choanoflagellates (the closest living relative to animals). It’s more likely, especially considering the other evidence, that microRNA arose twice independently, rather than microRNA being lost multiple times in the specific lineages that happen to make it look like it arose twice independently. The latter would be getting into “Satan buried the dinosaur bones to make it look like a natural process” territory!

This is post 8 of 49 of Blogathon. Donate to the Secular Student Alliance here.

My research part 2: MicroRNA evolution

Like I said previously, microRNA is typically highly conserved (have the same sequence) across animals because it’s involved in such important biological processes. But some microRNA isn’t conserved, which makes it particularly interesting. Is it not conserved because it just doesn’t have an important function? Is it not conserved because the divergent microRNA confers a specific fitness benefit to an organism? Or is it a rare mutation that leads to a disease like cancer?

That’s where my particular research comes in. I’m investigating microRNA variation within human populations and across the primate lineage. Here are some examples of interesting trends I may find:

  1. A microRNA is totally conserved across primates and other animals. This microRNA is likely involved in a really important biological process, like making a type of tissue.
  2. A microRNA is totally conserved within primates, but differs from other animals. This microRNA could confer some primate-specific trait.
  3. A microRNA is totally conserved within humans, but differs from other primates. This could be an example of “what makes us human.”
  4. A microRNA is not conserved at all. The more likely explanation is that this isn’t a functional microRNA at all. That’s the risk with working with such new data. Other types of small RNA can be erroneously labeled as a microRNA. MicroRNA is a specific class of small RNA because it’s processed in a very distinct manner and has a specific function.
We already know that there are some differences in microRNA between primates. In 2011, Svante Paabo’s group found a number of microRNA that were upregulated (present in higher amounts) in human brain, but not in chimpanzee brain. When they validated which messenger RNA these microRNA were targeting, they found the targets were involved in neural development. This is an exciting possibility for what shaped human brain evolution, but obviously still needs further testing.
The way my research differs is that I’ll be looking at how the sequence of microRNA differs rather than the amount. A sequence difference could totally change which messenger RNA is targeted, which is what ultimately affects the organism. I’ll be experimentally validating the effects of these sequence changes in a number of primates, including humans.

This is post 7 of 49 of Blogathon. Donate to the Secular Student Alliance here.

My research part 1: MicroRNA

My research studies a molecule called microRNA. Don’t feel bad if you’ve never heard of it, since microRNA is a fairly new discovery. The first microRNA was discovered in 1993, and the second one wasn’t discovered until 2000. We’ve discovered thousands of microRNAs by now, but they’re still not something all biologists are familiar with, let alone non-biologists. I know when my advisor initially suggested I study microRNAs, the first thing I had to do was go read the Wikipedia article. I knew nothing!

So what the heck is a microRNA? As the name implies, it’s a very short RNA found in plants and animals. Its function is a little more complicated, so let’s back up a bit. Most people have heard of the “Central Dogma” from their high school biology courses: DNA is transcribed into messenger RNA, which is then made into protein.

DNA serves as the “blueprint” for how to make an organism.The messenger RNA, which as the name suggests, serves as an intermediate messenger between the blueprints in the nucleus of a cell and the machinery out in the cyotplasm. Once in the cytoplasm, the messenger RNA is read by a ribosome, which produces a protein based on the instructions originally encoded by the DNA.

Messenger RNA can be made in varying quantities, and more messenger RNA leads to more proteins being made. The amount of proteins made is just as important as the type of protein being made. Genes are “off” if no protein is produced, and varying quantities of a protein can have profound effects on how an organism functions. This is why large chromosomal duplications are generally lethal or have major effects (like Down Syndrome) – with an extra chromosome contributing to protein production, protein levels are totally out of whack.

But the Central Dogma isn’t so dogmatic. This is where microRNA comes in. In animals, micoRNA functions as part of a protein complex called the RNA-induced Silencing Complex (RiSC). MicroRNA guides RiSC to a particular messenger RNA through complementary basepairing – the A in microRNA matches with a U in messenger RNA, the G with a C, etc. RiSC will then block from becoming a protein. RiSC can do this by directly degrading the messenger RNA, de-adenylating the messenger RNA’s poly-A tail to lead to degradation, or by recruiting other proteins to get in the way of translation into a protein. So when microRNA targets a messenger RNA, it results in that messenger RNA producing fewer proteins than usual. If enough microRNA is made, it may turn the gene off completely.

MicroRNA is especially important because one microRNA can have dozens to hundreds of messenger RNA targets. This means a single type of microRNA can have really profound effects on an organism. It’s one of the most important regulators of gene expression, and is involved in key biological processes like the differentiation of stem cells into specialized adult cells, cell proliferation, metabolism, and apoptosis (programmed cell death). Because it’s so important, most microRNAs are highly conserved across animals. This is also why microRNA has been heavily implicated in cancer – one small tweak can have drastic effects.

Stay tuned for more riveting information about microRNA evolution later!

This is post 6 of 49 of Blogathon. Donate to the Secular Student Alliance here.

The fear of getting scooped & the lack of communication within science

The fear of getting scooped really points to a larger issue within academia. Science is based upon the ability to test hypotheses and falsify data, which is why the open sharing of knowledge is so important. But fears about getting scooped lead to less open communication about methods and results. You don’t want to blab your results to any random person, or reveal too much preliminary data during a talk at a conference. You run the risk of someone running off with that idea and getting it done before you.

And because everyone holds their cards close to their chest, you often don’t know who’s working on similar research. Frequently the motivation to publish is the fear of getting scooped by a research group you didn’t expect. When new scientific papers are published, I always read through the titles in the Table of Content with some trepidation, hoping no one hits too close to my project. That would mean having to shift or completely revamp the focus of your research, which is one of the causes of people staying in grad school longer than expected.

It’s getting to the point where sometimes even published results aren’t immediately accessable to other scientists. Newly published genomes are often embargoed for a year so the lab that produced the data has more time to mine it. There’s a lot of debate over whether this is acceptable. On one hand, the lab in question often spent a lot of time, money, and effort sequencing that genome, and it seems unfair for someone else to swoop in and pick off the low hanging fruit questions. On the other hand, having that genome available is incredibly important so other scientists can judge its quality in order to more accurately interpret the results of a published paper, or to use it in their own research. What good is it to come up with all this knowledge about the universe if no one else is allowed to know about it?

I don’t have a solution for this problem with academic culture, but it’s something that gets brought up a lot. How do you feel about embargoes on genomes and other scientific information? For those of you who do research, have you had problems getting scooped?

This is post 4 of 49 of Blogathon. Donate to the Secular Student Alliance here.

On blogging about my research

The most frequent topic request I get for my blog is to talk more about my research. Usually the extent I talk about what I do is limited to vague tweets like “Yay, my code actually worked!” and “Why am I in grad school?” But people expect that a blogger who loves talking about science would be gushing about their own research. There’s two reasons I tend to avoid it:

1. Blogging is a a hobby and type of escapism for me. After working all day, I want to do something that doesn’t make me think of work for an hour. But more importantly:

2. Blogging about unpublished research is risky. I don’t want to give away too many details about what I do, because I run the risk that I’ll get “scooped” – that someone else will take the idea and finish it before me. This is even more likely with computational work, especially when using shared or public data. It’s not like I went out an found 1000 samples from rare frogs that no one else has access to – I’m just sitting in front of a computer. Some of the data I use will become publicly accessable by the end of the year, so I’m really pushing to get a paper out quickly. Don’t want to ruin my plan by having a big mouth!

But because you guys ask so persistently, I will blog a little bit about my research today. I’m going to focus mostly on the concepts I’m interested in and previous studies, but hopefully it’ll shed some light on my scientific interests.

This is post 3 of 49 of Blogathon. Donate to the Secular Student Alliance here.