Mystery Rays from Outer Space

Meddling with things mankind is not meant to understand. Also, pictures of my kids

July 1st, 2015

Why don’t I turn into a fish when I eat fish?

The question on Quora was:

Why don’t I turn into a fish when I eat fish? Or a cow when I eat beef?

The expanded explanation for the question was:

Before this is labelled as silly, here is explanation: there are specific chemicals in our bodies whose purpose is to prevent foreign genetic material in a body and cell from being read and translated into mRNA. What are the names of these chemicals and processes? How do they work?

My answer was:

Not a silly question at all, especially if we bypass the “eat” part and ask why just, say, injecting a fish cell into our arm wouldn’t turn us into a fish, or why giving our kid a transfusion of mongoose blood wouldn’t turn him into a speedy superpowered whizzer.

There are two parts to the answer.  First, DNA needs to have an elaborate support system before it can do anything.  It needs to be in a nucleus, wrapped in histones and other proteins, with access to polymerases and other enzymes, and so on and so on.  Just shoving DNA into your bloodstream doesn’t give it access to those things, so it can’t take over your cells to make fish or mongoose type proteins.

(But if you add to the DNA a system for entering a new cell and taking over the built-in systems, then you have a virus, which essentially does exactly that — turns your cells into a system for making more viruses.)

But why not a whole cell? Why can’t a fish cell settle down comfortably into our body and just pump out fish proteins all day long?

The answer is the immune system, which is aimed at identifying things that are not “self” — that is, that don’t match the template of our own cells — and to attack and reject them.  The immune system is very good at that, and can even reject very similar cells, like those of a different human, so identifying a fish or a mongoose cell is very easy to do, and those cells would be very quickly attacked and destroyed.

(Today, the immune system is tuned for identifying and destroying bacteria and viruses and so on.  But it’s possible that hundreds of millions of years ago, much of the immune system was tuned for exactly what we’re talking about here — preventing foreign cells from moving into the friendly environment and taking over.)

In response to a question in the comments (“What about plants and simpler organisms which don’t have complex immune systems?”), I added:

You have to get very “simple” in the simpler-organisms category before they lose the parts of the immune system that recognize different cell types, although the actual mechanisms are quite different in different organisms.

As for plants, they don’t reject foreign material, at least not in the same way that animals do; you can graft different plants, or even different species, together and they’ll grow pretty happily.  Grape vines and apple trees, to name just two, often have this done.

As to how, or even whether, plants reject a more subtle invasion by parasitic plants … I just don’t know.  Hopefully a botanist can answer.


June 29th, 2015

Is it true that only 5 percent of smokers get lung cancer?

The question on Quora was:

Is it true that only 5 percent of smokers get lung cancer?

My answer was:

It is not true that only 5 percent of smokers get lung cancer.

Source:  IARC Monographs on the Evaluation of Carcinogenic Risks to Humans  (…) Volume 83 (2004), Tobacco Smoke and Involuntary Smoking (specifically p. 167 in Chapter 2; there are also many other interesting charts on pp. 162-175, and useful tables from p. 177-263.

If a smoker quits by age fifty, then they still have a lifetime risk of over 5% of lung cancer alone.  Someone who continues smoking past that age has a much higher chance of lung cancer (up to 15% plus).

On top of that, of course, smoking increases the risk of many other kinds of cancer besides lung cancer, though not quite as much; so you’d probably multiply these risks by another 50% or so to account for the increased risk of bladder cancer, kidney cancer, esophagus cancer, etc.  So let’s say maybe 7-8% chance of smoking-related cancers for our hypothetical smoker who quit at 50, and maybe 20-25% for someone who smoked through his 70s.

And that’s all on the background of non-smoking-related cancers.

June 26th, 2015

Why did powered flight evolve only once in invertebrates?

The question on Quora was:

What’s the possible explanation for powered flight appearing only once in invertebrates and at least three times in vertebrates?

My answer was:

Interesting question that had never occurred to me before. I have a couple of thoughts, but these are just guesses.

(Edit to update: The premise of the question may not be quite right, because it’s been suggested that flight in insects has arisen multiple times:  Loss and recovery of wings in stick insects.)

First, what broad classes of invertebrates are there that could plausibly develop powered flight?  There are vast numbers of invertebrates, but things like corals, sea urchins, jellyfish, and so on aren’t really good candidates for developing flight.  We should only consider terrestrial species.  And then we should probably exclude things like the various types of worms; again, this isn’t a flight-friendly lifestyle.  So we’re left mainly with arthropods, and we have to exclude aquatic arthropods, and we’re left with mainly insects and arachnids.

But still: Why did insects only develop powered flight once (assuming that’s what happened, which I think is still a little unclear)? Why didn’t arachnids develop powered flight?

Maybe it’s a little unfair to blame insects for only developing powered flight once.  It arose pretty early, and there are lots and lots of insect fliers.  Some of the other lineages trying to develop flight later on would run into huge competition from the already well-adapted fliers up there.  But even so, it seems at first glance odd.

But maybe we gigantic humans underestimate the risks and overestimate the benefits of flight. The prevalence of mountain and insular apterism suggests that there may be a significant downside to flight among very small animals (i.e. most terrestrial invertebrates).  Darwin pointed out that island and mountain insects often lost their wings, and argued that this might be because flying insects would risk being blown out to sea, or away from their mountain, so that there was a benefit to remaining firmly attached to the ground.  Others have also suggested that aptery might have metabolic benefits in harsh environments, reducing heat loss, for example.  So the advantages of flight in many environments might be overstated.

The benefits of flight are also potentially lower for very small animals, since they have essentially no risk from falling.  Unlike larger animals, insects can carelessly launch themselves into space from any height and land safely.  So there’s a large class of benefits that invertebrates don’t gain.

Still, there are benefits of flight, even for tiny things.  We’d point to dispersal as a major one, and then to avoiding predation, to predating on other things, and to long-distance foraging as a fourth.  So: Why aren’t there flying arachnids, say?

Well, there are flying arachnids.  Ballooning spiders have developed a complex set of adaptations that let them travel for hundreds of miles.  It’s not “powered flight”, but it serves the same purpose of dispersal.

(And stretching the point even further, we can point to parasitic worms and so on that force their host to be eaten by birds, and to aquatic invertebrates that attach their eggs to waterfowl feet, thus attaining flight and dispersal in a very indirect way.)

Avoiding predation and predating on others falls into the category I mentioned above — because insect flight arose so early, attempts at either of these would run into ferociously well-adapted flying predators already, either as competition or as threats (or both).

So the one benefit that’s left is long-distance foraging, and that really only makes good sense to social insects, where long-distance travel and return is beneficial.  There aren’t many social things, and of them only bees and wasps (that I can think of) use this strategy (ants and termites use flight for dispersal only).  So it’s a highly specialized approach that probably isn’t useful for most things.

So at the end of the day, maybe the answer is that we as humans overrate the advantages of flight to a tiny thing.  Most invertebrate lifestyles won’t benefit from flight, and those that would either have developed flight already, or faced too much competition by the time it would be useful.

All speculation, and I’d be interested in hearing better ideas.

June 24th, 2015

Are there any proteins that, when sequenced, have segments that spell English or colloquial words?

The question on Quora was:

Are there any proteins that, when sequenced, have segments that spell English or colloquial words?

My answer was:

A typical protein is about 350 amino acids long.  I am not aware of any English or colloquial words that are 350 letters long.  Very few, if any, functional proteins are less than 20 amino acids long, which is still very long for English words.

Many protein sequences contain within them English words and names. ELVIS can be found in many proteins, but ELVISISALIVE hasn’t turned up yet.  CRICK can be found in many,  FRANKLIN appears once in a hypothetical protein from Treponema primitia (WP_010253273) and of course WATSON is impossible.

What’s the longest English word that can be found in the GenBank protein collection? Offhand, I don’t know (and it will change on a regular basis, at the rate the collection is growing).  I bet I can find it in a few lines of code, though, and if no one beats me to it I’ll take a shot at it tomorrow; it’s too late tonight.

Update: The longest more or less English word I can find in the human reference sequence protein database is “TARGETEER”, 9 letters long.  It’s found in several isoforms of “C12orf42″, e.g. uncharacterized protein C12orf42 isoform 1 [Homo sapiens].

I only looked in the human reference sequence library, not the complete protein database for NCBI, which would have taken too long for download (too long for the mild curiosity I had, anyway).  This database has 72,204 protein sequences in it, with a total length of 46,315,661 amino acids; average protein length 636.4, median length 467.0, geometric mean length 468.5, distribution looking like this:

For words, I used the builtin unix dict (on my computer, /usr/share/dict/words), which contains 235,886 more or less English words ranging from 1 through 24 letters long (THYROPARATHYROIDECTOMIZE, TETRAIODOPHENOLPHTHALEIN, SCIENTIFICOPHILOSOPHICAL, PATHOLOGICOPSYCHOLOGICAL, and FORMALDEHYDESULPHOXYLATE, if you’re playing Scrabble).

“TARGETEER” was the 119,925th-longest word in the dictionary, and since I started with the longest and worked down it was over halfway through the dictionary (50.8%) before I got the first hit.  All in all, it took close to an hour to run in the background, with no attempt whatsoever at optimizing the script.

June 22nd, 2015

What evolved first in bats, flight or echolocation?

The question on Quora was:

What evolved first in bats, flight or echolocation?

My answer was:

It’s not clear. A 2010 paper suggested that the oldest known fossil bat was capable of echolocation.  Earlier work on the same fossil had argued that it did not echolocate, which would have been evidence that flight came first.  But if this bat ancestor did indeed echolocate, the answer becomes unclear:

The relationship between echolocation and flight in the origin and adaptive radiation of bats remains a topic of discussion. Presently there are three schools of thought: the first proposes that echolocation evolved before flight, the second proposes that flight evolved before echolocation and the third proposes that flight and echolocation evolved synchronously. … Our data do not resolve these questions …

A bony connection signals laryngeal echolocation in bats

A large group of modern bats (the megabats) do not echolocate, but that doesn’t help resolve the question; it could be that echolocation arose after mega- and microbats diverged, but it’s equally possible that megabats lost the ability to echolocate after they diverged.  Since non-flying mammals (e.g. shrews) are capable of some echolocation, there’s no reason to believe that flight had to precede echolocation.

A more recent study on bat relationships finds hints that echolocation arose multiple times in bats, which would argue that flight came first, but even this study can’t clearly determine whether echolocation arose multiple times or was lost in some groups:

… our findings prove without doubt that the evolution of laryngeal echolocation in bats has involved either multiple acquisitions or an evolutionary loss in Old World fruit bats

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

June 19th, 2015

Earthworms are an invasive species in North America

The question on Quora was:

Is it true that an invasive species of worms arrived in North America with the early Europeans and changed much of the continent’s ecology?

My answer was:

Yes, it’s true.  Earthworms aren’t native to North America, and they’ve done significant harm to North American ecology.

The invasion of European earthworm species across northern North America has severe impacts on native ecosystems.

Warming shifts ‘worming': effects of experimental warming on invasi…

These patterns suggest earthworm invasion, rather than non-native plant invasion, is the driving force behind changes in forest plant communities in northeastern North America, including declines in native plant species, and earthworm invasions appear to facilitate plant invasions in these forests.

Earthworm invasion as the driving force behind plant invasion and c…

Our results provide regional evidence that invasion by Lumbricus species may be an important mechanism in reduced plant-species richness and changes in plant communities in mature forests dominated by sugar maples.

Effects of earthworm invasion on plant species richness in northern…

(It’s more widely known that the introduction of honeybees around the same time has also devastated North American ecologies, to the point that we don’t even know what the natural ecologies were before the introduced bees drove the native pollinators extinct.)

In a comment to the question, I was asked whether earthworms and honeybees are beneficial.  I said:

It’s context-dependent.  For example, honeybees have driven many native North American pollinators extinct. That means that honeybees are required for pollinating lots of things. Are honeybees beneficial? Well, they’re essential, but they wouldn’t be essential if they hadn’t killed off their competitors.

Same with earthworms.  Are they beneficial in your garden? Absolutely.  Are they beneficial in the boreal forests that they’re invading? Not if you want to keep the forests as they are.  So it depends what you’re asking.

June 17th, 2015

How vulnerable are salamanders to cancer?

The question at Quora was:

How vulnerable are salamanders to cancer?

My answer was:

There aren’t many large-scale epidemiological studies of cancer in salamanders and newts (urodeles), but they certainly get cancer, and the overall picture is that they are intermediate in their susceptibility to it.

Anuran and urodele amphibians develop spontaneous neoplasms in all major organ systems with the integumentary system a frequent target. … Anurans seem to have a greater frequency of spontaneous neoplasms than do urodeles …

Amphibian tumors: a comparison of anurans and urodeles.

Incidence of pigmented skin tumors in a population of wild Montseny brook newt (Calotriton arnoldi).

As well as these population studies, there are a reasonable number of case reports of tumors in urodeles as well.

June 15th, 2015

The Cameron Highlanders, the Faroe Islands, and multiple sclerosis

The question at Quora was:

Did the Cameron Highlanders bring a cold virus to the Faroe Islands in WW2 that damaged the immune system and the testicles and ovaries of the Faroe islanders and make them vulnerable to multiple sclerosis?

My answer was:

A leading hypothesis for the cause of multiple sclerosis is that it’s an autoimmune disease that starts with a genetic predisposition, that’s triggered by a viral infection.  It may be a specific virus, but it’s more likely that it can be triggered by any of a wide range of viruses, which may be innocuous on their own and require other genetic and environmental factors to cause MS.

The timing of MS on the Faroe Islands shows a dramatic increase starting in 1943, and waxing and waning over multi-year periods, consistent with a role for an infectious agent:
Multiple sclerosis: variation of incidence of onset over time in the Faroe Islands.

It’s been suggested that British troops spread a very mild virus among the inhabitants that led to the disease among the inhabitants:
Epidemiology in multiple sclerosis: a pilgrim’s progress.

The hypothesis is controversial, and other researchers raise evidence opposing it and supporting a genetic role:
Multiple sclerosis in a family on the Faroe Islands.

However, neither hypothesis seems to fully account for the possibility that both genetics and infectious diseases could be critical factors simultaneously.

In any case, I don’t think that “immune system and the testicles and ovaries” are proposed to be primary targets.  I think the model, such as it is, suggests that the primary infection damages nervous tissue and leads to an immune response against the nervous tissue components when people have a certain set of genetic tendencies.

June 13th, 2015

Questions and answers

Since I’m no longer doing the question/answer thing at Quora, I’m going to move some of my answers over here at intervals.

March 17th, 2014

Influenza subtypes in birds

What subtypes of influenza are found in birds?

Influenza is naturally a disease of wild waterfowl; humans, like dogs, chickens, and whales, are occasional victims of mutated viruses from this vast global reservoir of viruses.  In wild birds, flu viruses reassert and recombine wildly, mixing almost all the known subtypes promiscuously.

There are 18 known hemagglutinin subtypes and 11 known neuraminidase subtypes. Two of each are only known from bats, so there are 16 and 9 that could occur together in birds, for a total of 144 possible combinations.  Some subtypes of each are rare, and some HA and NA types don’t play well together. Which combinations have been found, and how common are each?

Mainly because I was playing with Plotly,1 I tried making a bubble chart of HA and NA subtypes found in waterfowl throughout history.  I used sequences in the influenza databases, sorted by HA and NA, and plotted them with HA on the X axis, NA on the Y, and size of each bubble representing how common they are.

Of course, this is not really a representative look.  It’s wildly distorted by surveillance trends; people intensely test birds for H5N1 (because it’s lethal to humans), and H7N7 was surveyed mainly after multiple people were infected in the 2003 outbreak in the Netherlands, so those are probably over-represented compared to their actual prevalence in birds.  Still, it helps give a sense of the complexity of the viruses circulating out there.

Flu in birds


  1. My conclusion: Plotly is pretty cool, but doesn’t offer me very much.[]