A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes

When I was given permission to Telework, I was worried without the ninety or so minutes of time commuting each working day I’d never be able to read all twenty or more books I normally read in a year, or for that matter the next book following The Thing with Feathers: The Surprising Lives of Birds and What They Reveal About Being Human. But, rest assured, cleary I did and now I’m here to talk about it.

Adam Rutherford, no relation to Ernest, weaves an interesting survey of what Deoxyribonucleic Acid has contributed to our modern understanding of biology. He starts off talking about how humanity is like a braided stream, with genetic lines splitting and then re-emerging between Homo Neanderthalis, Homo Denisova, Homo Floresiensis, and other potential Hominin people lurking around Eurasia around the Wisconsin Glacial Period.

He then talks about how in ancient times, Europe was united under various different tribes, some coming from the East, some coming from the South, and how Europe was transformed by these migrations and that most Europeans today are descended from those Eastern Invaders and in that sense Europe was united long ago, when we were still in the Upper Paleolithic, until the advent of Agriculture in the Neolithic Age.

Next, Rutherford investigates the origin of the American Indian cultures. He tells the story of Kennewick Man in much detail and why it’s so hard to get American Indians to consent to being genetically sequenced. Despite these difficulties, he does show that American Indians all probably descent from a single migration over the Bering Strait and how the Inuit have genetic modifications for low oxygen environments, similar to the Tibetans.

The next part gets a little heady. The idea that we are all descended from Charlemagne isn’t too hard to believe but the idea that we could be descended from folks from the Andaman Islands or Australian Aborigines seems to be pushing it. When you think about it, the base logic is correct. Going back twenty generations you have over a million man great grandparents, and over thirty you have over a billion. Clearly, if each generation averages twenty years, in six thousand years time you do have in theory one billion ancestors, but as there wasn’t a billion people six thousand years ago, clearly there must be some inbreeding. Not necessarily first cousin inbreeding, but maybe seventh or eighth cousin a remove or two would be commonplace.

The problem is when you think that this implies that everyone alive back then who had a child must be your ancestor is a false premise. One can guess the amount of inbreeding, but in truth, it’s possible, and even probable, that the inbreeding is even tighter than the whole population of six thousand years ago. It seems more logical, even if the clusters of today are different than the population clusters from back then, that the Australians at least were isolated until 1606, when Europeans started coming there. With only four hundred years contact, I’m highly dubious I’m descended from a single Aborigine from six thousand years ago, despite many of those Aborigines having descendants alive today. Charlemagne, maybe, but not everyone who ever lived six thousand years ago.

I did, however, like the story of Richard Ⅲ‘s discovery and it’s comparison to the insane idea that we could find Jack the Ripper in a used hankie. Great presentation of how to do bad and good science. The discussion of Francis Galton was also interesting, as there is stuff to admire the statistical genius with so much racism in his heart.

The topic of Race was an interesting one As Rutherford is half-South-Asian, I know that he would have suffered discrimination in the United Kingdom and of course feel for him. As a half-Jew, I have noted very little Jewish discrimination in the United States, apart from tourists from Europe, but when I do go to Europe, especially the farther East I go, I do notice a distinct hint of Anti-Semitism there. Nothing to write home about, just the random bloke who clearly has a problem with my nose.

However, I will say I think it’s excellent the way Rutherford points out there are more differences within race than there are distinguishing genetic characteristics within a race. I would, though, love to have red hair—well, to be honest, I’d love to have any hair, but that’s another story.

The discussion of SNPs and GWAS. There’s a great discussion of why it’s so hard to find the causes of diseases. After all, it’s very unlikely a SNP change in a single protein expression will change a behavior. And even the known genetic defects can have gene modifiers. The discussion of how heritable certain characteristics are was also fascinating. And the definition of epigenetics was a great new wrinkle. The only element missing is the influence of the bacterial flora that also influences our behavior.

Finally, it was nice to ground us in what evolution can and cannot do. The HOX Genes discussion was fun, as I do like the idea of a HOX d2 gene added to make a great story. And also, it’s interesting that GWAS can’t find an evil gene. I still blame testosterone for much of the evil in the world, but clearly even that hormone can’t be the only element at the root of modern violence. Indeed, if we could eliminate child abuse, we would go a very long way to solving many of what ills our society.

In summary, genetics is a wonderful tool in the development of biological understanding, but I wonder just what our current trends in slow evolution will bring. Only time will tell.

A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes
A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes

Next up, The Remedy: Robert Koch, Arthur Conan Doyle, and the Quest to Cure Tuberculosis, another book without a commute, with three weeks to complete…

Hope to see you in person soon, my sapiosexual friends!

Relax—you actually don’t need to sanitize your food

On Sunday, I posted an article about sanitizing your food after you return from grocery shopping. The thing is, the medical professional who posted the original clip went a bit overboard in terms of how sanitary he felt he needed to keep his food once retrieved from the grocery store. The truth is, not everything the doctor says in his video is strictly correct and he is no food safety expert, as has been pointed out to me. However, for the most part my textual commentary doesn’t contradict what I’m about to share and I am happy to give Dr. Don Schaffner his due:

Buckle up, readers, as it’s about to get serious! Thirty-two more tweets, seriously!

Unfortunately, the link above to my original article with take you to that video but if you haven’t hit play on the video, and just read my commentary, you should be fine. Please, trust Dr. Don!

Sometimes I roll my eyes at my fellow writers when they they try to come up with Science Fiction ideas, since I did study undergrad Physics and read a lot of science books. I feel you Dr. Don!

Here here! I already outlined most of what was right in the video in my original post. I think I may have misspoken on how to wash produce but I’ll save that commentary for later.

There’s a bit of nuance to this, but what the good Dr. Don is saying is there is a difference between a random but not yet denatured strand of viral RNA, which in itself isn’t particularly harmful—at least, not infectious—where as a live virus was not observed. As in, the crown-like outer shell of SARS-CoV-2, a.k.a. the Coronavirus, the “Crown Virus”. Without the outer shell and crown-like protrusions, the virus has no way of penetrating cells, be they eukarya, bacteria, or archaea. Note, this pathogen only infects eukaryotes, though most viruses are harmless, only infecting bacteria.

More fundamentally, though, Dr. Dan points out that the CDC Study that came up with the 17-day number for RNA was never published in a peer-review paper where the methodology and techniques used could be scrutinized and dissected. Without the process of peer review, the observation is as good as anecdotal.

This was one of my biggest beefs with the video too. I mean, it’s one thing in the winter in Lansing, MI, where the outside might already be the temperature of your freezer. But that won’t work in Florida, not by a long shot. So unless you’re gonna be like Thomas Jefferson and truck in ice from Canada to keep your food from spoiling, don’t leave your perishable food in the garage!

Exactly!

This is a very good point. One of the ways the SARS-CoV-2 deactivates is through desiccation. If the virus is in a medium that allows it to dry out, it will no longer be effective. This is why spittle from sneezing is the most dangerous.

The virus is highly communicable, to be sure, but its transmission with respect to someone with the virus touching an item on the shelf, putting it back, and then having you grab it is exceedingly unlikely. And by the time you get to it, it’s quite likely SARS-CoV-2 has already dried out and perished.

I have to agree, as different packaging materials will allow the virus to remain active long than others, and again, as state above, it’s unlikely by the time you pluck the item from the shelf that it would still have any active virus on it even if it had once.

Washing your hands before eating should be second nature anyway. As Dr, Don says, you can remove the item from the packaging, put it on a clean plate, and then wash your hands before eating and any contamination on the packaging will have been removed from the equation.

Wørd!

There are good reasons not to use soap to wash your produce and I will admit I got that wrong before. Soap dissolves cell membranes and while most produce is covered by dead epithelial cells—like those on the outer layers of your skin—and thus won’t likely cause cellular damage to your food, but if you slice the food it could spoil its flavor and if you fail to wash it all off and it gets in the nooks and crannies of your consumables, Dr. Don is right, you’re itching for a tummy ache. The oily residue soap normally removes isn’t a big issue on produce and thus a simple water bath should be sufficient for cleaning your produce.

Precisely!

Even the prescient Dr. Ignaz Semmelweis knew that hand washing wasn’t a panascia. It reduces the change of killing a mother giving birth, but even if done right, it isn’t perfect. Soap and water are great for removing both hydrophobic and hydrophilic substances from your person, but not every pathogen is removed by such reactions. SARS-CoV-2 is damaged because of its hydrophobic coating, but the same isn’t true for all toxic substances.

Indeed, human skin has many friendly microbes that help keep the skin clean and fresh. You wouldn’t want to boil those off anyway, even if you could. Love your friendly microbes. Just use soap and water to kill SARS-CoV-2. That M*th*r F*ck*r must die!

This is another good point. Not all handwashes are equal. I try to do a rather complex technique when washing my hands which I may document another day, but the long and short of it is, just rubbing your hands together isn’t enough, and even my technique isn’t one hundred percent effective.

Great point! Early food preservation in wine bottles with their tartaric acid may have worked for Napoleon’s army, but when we started using steel and aluminium cans, or even glass, we had to be very very sure everything was sterile. Watch any number of episodes from Comment C’est Fait (How It’s Made chez É-U.) to see how this is done.

Remember the words of François-Marie Arouet, a.k.a. Voltaire, “Le mieux est l’ennemi du bien.” (Perfection is the enemy of good.)

This is one point I did make in my original article. Glad to see my point is backed up by Dr. Don.

This one is simply a caveat emptor. Don’t assume a product can kill viruses. Indeed, there are many ways product makers can use language that makes it seem like it’s effective against pathogens, but unless there is peer reviewed literature to back it up, sorry, it’s not magic. It won’t protect you against SARS-CoV-2 any better than simply washing your hands.

There is something to be said for the security blanket of feeling better. But, yes, they won’t help and are no better than a simple cold-water bath.

Or for treating the fabric of your home made N95 mask.

I like using reusable bags and agree washing them like any fabric is a wise idea. If you must use disposable bags, please use ones that are recyclable or compostable.

In other words, keep your bags close but be more mindful of social distancing and that the bagger uses proper sanitary techniques. But again, the likelihood that someone with the virus has used that same checkout stand recent-enough for the virus to still be active is very likely, and most grocery stores, like Wegman’s will do their best to sanitize the checkout counter between each customer during Covidapolis.

Keeping them in your car is a good idea. I always keep my MOM’s Organic Market bag in my car so it’s ready whenever I go there.

Wash your hands!

I have indeed noticed Wegman’s doing just that. They are, IMHO, doing a great job!

Know what you want, like Low Acid Orange Juice, and head straight over. Keep those two meter buffers to keep safe!

If you can get hand sanitizer, then it’s great when there isn’t soap and water available. But when you have soap and water, always prefer that.

Done in the most complete way possible Dr. Don!

Shelter in place, y’all, and use Zoom to see a friendly face!

Much obliged Dr. Don! Happy to help promote good science, sound food handling, and how to weave a great yarn, and sew a great mask!

Bon appetit, mes amis!

The Copernicus Complex: Our Cosmic Significance in a Universe of Planets and Probabilities

Because of the issues with #CO2Fre’s tyre, it only just finished this book in time for our meeting today.

I started this book right after finishing 18 Miles: The Epic Dreams of Our Atmosphere and Its Weather. Overall, I found the book a bit repetitive but it does bring up some interesting topics. I think the conclusion of we being born of both order and chaos is a nice ides given other books I’ve read that go into great detail on how unusual it is for biologic life to arise and how even more astronomical the odds are that a bacterium would take up residence in an archaea to make eukaryotes.

The survey of extrasolar planetary configurations was fun, however. I love the description of unusual systems like tight packing of planets, binary star systems, and life evolving on a Gas Giant moon. Although there are multiple ways a binary star system could have planets. For instance, one could have one star is a large (but not huge) one like our sun, and the other is a red dwarf, a bit larger than Jupiter, with the planet orbiting only the major star. But what Caleb Scharf seems to present is something more akin to two stars of relatively close mass orbiting one another tightly and a planet much farther out which orbits them both. In the later case, the idea that suns eclipse each other in regular cycles making the nature of a solar-centric universe much more amenable to budding intelligent life was a great and interesting flight of fancy that will help inform my better authorship of Science Fiction.

My main nit goes back to the first issue, though, with the mention of Antonie van Leeuwenhoek in the prologue. I thought the author did better introducing astronomical elements than he did biological elements and it was in the biological sections in which I was bogged down.

I am happy though to concede that with the modified Drake equation: \(N = R_* \cdot f_p \cdot n_e \cdot f_i \cdot f_e \cdot f_i \cdot f_c \cdot L\) where,

  • \(R_*\): the average rate of star formation in a galaxy
  • \(f_p\): the fraction of those stars that have planets
  • \(n_e\): the average number of planets that can potentially support life per star that has planets
  • \(f_i\): the fraction of planets that could support life that actually develop life (like bacteria or archaea) at some point
  • \(f_e\): the fraction of planets with life (like bacteria or archaea) that develop complex life (like eucaryotes)
  • \(f_i\): the fraction of planets with complex life (like eucaryotes) that actually go on to develop intelligent life (civilizations)
  • \(f_c\): the fraction of civilizations that develop a technology that releases detectable signs of their existence into space
  • \(L\): the length of time for which such civilizations release detectable signals into space

We know \(R_*\) is about three percent more stars per year, and that \(f_p\) is often greater than one, perhaps an average of four in modern surveys. \(n_e\) is a little harder to determine as we generally define it as a goldilocks zone, but as the book points out, life with radically different chemistry could have a different universal solvent than water. Methane, CH₄, for instance. \(l_i\) is a harder one but it seems this may indeed be quite common in any planet large enough to have plate tectonics and a hot core. The harder question is if \(l_e\) is common or not. As we don’t exactly know how eucaryotes evolved or, more specifically, how such a symbiosis could evolve so stably without consuming it. Finally, \(f_i\), \(f_c\), and \(L\) are all based on how intelligent life evolves and sustain itself, which, again, we have only one data point and can’t draw any conclusions from that at all. The main point though is we are getting closer to answering the first five terms at least and all are looking, even \(f_e\), a bit like we are not alone.

One of the most interesting aspects, however, were the Zodiacal Light display. I never knew that was possible and now I definitely have it added to my Bucket List. It was fascinating to learn about all the planetary and extrasolar debris that just sits along the ecliptic plane. And I enjoyed the author’s discussions of the origin of our solar system and how it compares to the many other stellar systems possible.

Talking about how Copernicus made our universe more knowable by virtue of it being ordinary and nothing special was a great way of presenting the conundrum between Anthropocentrism and ubiquity implied by Copernicus. I think that is the most important conclusion: that we are both special and ubiquitous. That our journey to intelligent life was unique, but that there are many ways of for the universe to know itself, and we are only one of those ways.

The Copernicus Complex: Our Cosmic Significance in a Universe of Planets and Probabilities
The Copernicus Complex: Our Cosmic Significance in a Universe of Planets and Probabilities

Overall, the text could have been tighter and less repetitive but the overall conclusion seems sound. We are, indeed Unique and Ubiquitous. Now, on to, The Thing with Feathers: The Surprising Lives of Birds and What They Reveal About Being Human

See you later, my friendly fellow sapiosexuals!