The Most admired people in 2020

 

In two polls reported for the most admired people, Barack Obama and Michelle Obama were the most consistently regarded.

 

To be precise, Barack Obama came first worldwide, and first or second in the US, depending on the poll. In Australia and the UK, he was beaten by David Attenborough.

Michelle Obama was the most admired woman worldwide, and in both US polls. In the UK, Queen Elizabeth II ranked ahead of her; in Australia, both the Queen and Jacinta Ardern ranked ahead. Ardern was top in New Zealand, unsurprisingly, followed by the Queen and Obama.

Donald Trump beat Obama in one of the US polls - but that’s because it was taken at a highly politicised time, and the Democrat vote was split, with Obama coming in second, and Joe Biden third. Trump was supported by 18%, Obama by 15%, Biden by 6% and, interestingly enough Bernie Sanders by 1% (7^th most admired). It’s quite salient to find that Obama outperformed Trump in every country surveyed - except Russia. They have a friend in Trump!

 

In Australia, only two Australians made each list: the prime minister, an athlete, an actor... and a previous prime minister, Julia Gillard.

 

Of the top 20 men globally, 35% (7 men) were leaders/politicians, 20% were athletes, 20% actors, 15% capitalists and 10% spiritual leaders. I might have expected a more eclectic mix, but that gives some idea who people look up to the most: leaders and achievers that are in the public eye. People admire their power, admire them physically, or admire their wealth. There’s a 12.5% exception for their humanism, if you count Bill Gates as half philanthropist.

 

The Australian list was similar, but we admire leaders less (25% instead of 35%) and sports people more (25% instead of 20%) - which suggests we have the same regard for each! David Attenborough was an addition and exception. Is he admired as a scientist or a humanist? Possibly more of the latter.

 

The methodologies for the surveys need to be mentioned. In the US, Gallup surveyed in December, and asked an open-ended question, which meant people could choose personal acquaintances.. For the rest (including the other US survey), 42 countries were included (which included Turkey - so Erdogan got to the global top 20, although two Turkish figures were ahead of him within Turkey, both singers). YouGov did some preliminary polling earlier in the year, then asked the survey questions from a closed list of people.

My List? Off the top of my head, I’d include

 Jacinta Ardern

 Julia Gillard

 Barack Obama

 Bernie Sanders

 David Attenborough

If I wanted to include entertainment, I might include Neil Young (for his enormous. varied musical career and great guitar work), George Clooney (for his humanitarian as well as screen presence) and Patrick Mahomes (US quarterback for the KC Chiefs, for his ability and leadership). If pressed, I might come up with more names from science, literature, music and American Football.

 

And what is admired? The list of qualities seems to differ, depending on whether the involvement is personal, work-related, or those with no direct connection.

The following list appeared in Forbes, which might speak to leadership as much as anything:

 

1. Humility

2. The ability to learn

3. Integrity 

4. Responsibility

5. Resilience

6. Compassion for others

7. Respect for others

8. Big vision

9. Inspiring others

10. Reinvent ourselves

 

Homo floresiensis redated: the long game

The new discovery of further Homo floresiensis remains adds to our body of knowledge while asking as many questions as it answers.

The most significant new information is that floresienses had been on that small island from 700,000 to 55,000 years ago (at the minimum range).

Scientific consensus seems to be that they are a species of Homo.  Although their small stature is suggestive of the Homo predecessor Australopithecus,  it is instead due to insular dwarfism - which means that 700,00 years ago it was already long enough on that small island for it to have evolved smaller to match the scarcity of resources there.

That's an awfully long time to be stuck on an island!  They certainly didn't do much with their time there, compared to the achievements in the span of modern humans.  That indubitably reflects their smaller cranial capacity.

Yet before we disparage a long-static lineage, we need to remember that any such species has to be said to be well-adapted to its environment.  On that basis, they were better adapted than most hominin species, with current evidence showing a lengthier stay on this earth than most others.  That longevity may reflect the stability of the Flores island environment, with little competition from apex predators or other hominin.  Yet it has been said that on available evidence, they disappeared at around the same time modern humans passed through on the way to Australia.  That could be a giant coincidence of the specimens unearthed to date, but it reflects an apparent pattern of Homo sapiens' interaction with other hominin species.

My current questions:

What discussion does this open up about stasis?  There's a lot of possibilities.

Did floresiensis last any longer than 650,000 years?

Were they evolved from Homo erectus?

And in particular, since the original find was entirely due to Mike Morwood seeking an understanding of the migration story of the first Australians, what's the full story of hominin migration between Africa and Australia?  The fossil record suggests there is an awful lot more to be gleaned from digging up all the islands in Indonesia.  Let's hope the past disputes lead to more successful governance of future projects

Fear and the devil in natural history

  Reportage of natural history is sometimes fraught with miscommunication.  Maybe the writer doesn't understand the subject or doesn't express themselves properly.  At other times, the devil is in the headline and the detail contains the light.

For all their effort to produce items of interest in natural history, The Guardian [Weekly] has something of a tract record for purveying conceptual misunderstandings.  I remember a recent example where the writer perpetuated a common mis-phrasing of natural selection to suggest the organism (a tree) intentionally evolved in a particular direction, rather than being the surviving mutation of those subjected to the environmental pressures.  A subtle but important distinction.

In the GW of 18th March 2016, an article by Sarah Kaplan was headed Why nature needs a landscape of fear, with a subtitle: Dread of a predator can often have a beneficial impact on the environment.  Hold it right there.  Some natural environments may change radically with the sudden introduction of an apex predator.  Other environments, with the removal of a key predator, may be thrown out of balance.  But the ipso facto presence of a significant predator is not a necessity for balance in a natural environment.

The New Zealand environment, for example, was the product of millions of years of absence of significant predators.  Under such conditions, avian flight proved an evolutionary burden, and in the absence of predator pressure, a significant number of bird lineage gradually lost the capacity of flight.

The Guardian article is based on a study by Justin Suraci (University of Victoria, in Canada) into the changing behaviour of fauna with the introduction of predatorial noises to environments which once had predators - before the heavy hand of humans intervened.

We have reformed the planet in our image, moulded it for human needs.  We only suffer domesticated flora and fauna, and reduce Earth's original environment to islands - prisons - of wilderness.

A notable example given of the reversal of this process was the reintroduction of grey wolves to Yellowstone National Park - one of those island prisons.  The effects - not just from direct predation - cascaded down the food chain, restoring past balances both faunal and floral.

But nature does not need a landscape of fear.

The article was sourced from the Washington Post.  I tracked down that original: it's headed Dread is vanishing from the animal world.  Here's why it's a bad thing.  A far more accurate account of the contents of the article.

And so the answer is that the devil has been guiding the hand of the Guardian Weekly's subeditor.  While not the exclusive domain of the devil, this is one in which he often lurks close by.

Sinus Solution

I've had chronic sinus problems all my life.  Now I've found a solution, at least partial.

Sometimes I've had particular problems breathing through my nose in bed at night.  I've noticed it's been more likely to be a problem in winter.  Summer has been much less of a problem, although the pattern has been quite obscured by other factors, such as colds - which for me come on more in autumn than winter - and allergies.

Recently this winter, I started wearing a woolly hat to bed at night.  And it's worked a treat.  I've been able to breathe through my nose most of the time at night, and my sleep has been less disrupted.  This effect is definitely unrelated to viral colds, where congestion changes over the course of days, not hours.


It's easy to say that's obvious: much of our body heat is lost through the head, and since my hair is quite short I'd clearly suffer more than average in that respect.

Yet the link between losing heat and sinus congestion is not clear.  I have discussed sinus trouble with a number of doctors, and one or two specialists - none of them has mentioned the idea that local temperature in the head can affect congestion.  I've not heard of the connection in literature either.  Doubtless it's been broached in the past, but anecdotally it doesn't seem to be ready knowledge in the medical fraternity.

The nose fulfils a number of biological functions - smell is only one of them.  In an evolutionary sense, there is variability simply because of its function as a temperature regulator: living further away from the equator favours longer noses, to help warm the incoming air; such function is not needed by humans closer to the equator, and noses tend to be broader and flatter.  That it acts as a general heat preserver does not necessarily say much about the heat exchange at a local level.  Maybe for me there's a more marked local heat exchange effect than for many other people.


This is conjecture.  All I can say with certainty - so far - is that I'm experiencing incontrovertable improvement in nighttime breathing through the nose by wearing a woolly hat to bed at night.  The effect is somewhat less pronounced during the day - perhaps because I travel in and out of airconditioned environments frequently enough to make the effects less obvious.

 So far, internet searches have turned up just a single reference to this issue - on a forum about hats.  There were several anecdotes about wearing a hat easing sinus congestion.  Just one of those comments mentioned medical advice to do so - by a surgeon, after a sinus operation.  So the truth is out there, but not well known.

I'm keen to hear of other experiences.

Word of the day: copepod

A copepod is a type of crustacean.  It might make you think of arthropod, the phylum (body type) that crustaceans belong to, but the prefix -pod means foot, of course.  The name copepod comes from Greek, meaning oar- or handle- and -foot.

The copepoda are actually a subclass, in the Linnean classification.  Which mainly means there are quite a few species of them.

If you look at the photo in the Wikipedia entry, it actually looks like plankton.  I didn't know crustaceans could be planktonic - or vice versa.  There you go.
However, plankton is just a general term for small marine life (either animal or plant) that lives near the surface of the ocean.  So things that feed on plankton are just feeding on... "stuff".

 And now to what brought me to this word (something Wikipedia doesn't mention): some species of copepod are bioluminescent, meaning they emit light.  The actual mechanism involvese a combination of two substances: luciferin, a pigment that reacts with oxygen; and luciferase, an enzyme (a protein catalyst).  Interestingly enough, this very mechanism has evolved separately in a several different organisms, including fireflies and anglerfish.  I guess it shows that this kind of mutation is:
a) useful
b) not too hard to arrive at (for example, just a couple of point mutations).


 Where did I encounter this word? A few days ago, on the bus.  In New Scientist (12 May 2012); another word I'd never seen before.

Word of the day: Chevrotain

Another word with evolutionary significance.

 Chevrotain 

A chevrotain is also known as a mouse deer (which can be somewhat deceptive).  The name comes from French, and roughly translates as 'little goat'.

It does look halfway between a mouse and a deer, but it's more meaningful to think of it as a very small deer: you couldn't get a real-life mix between a rodent and an ungulate (they're clearly genetically too distant).

They're actually a group of species (called a 'family' in the old, Linnean classification) found in Africa and Southeast Asia - with some variation in appearance between species.  This grouping includes the smallest ungulates in the world.
The rodent features are misleading, and would be an example of convergent evolution - that is, unrelated animals that evolves similar features for similar environmental niches.

Where did I encounter this word?  This is what makes this species significant: recently there was a Wikipedia feature article on giraffes.  They're (even-toed) ungulates - which evolved from creatures that looked rather like this 54 million years ago.

Word of the Day: Ungulate

First: Why?

Why something as staid as Word of the Day?

It arose from a comment someone made to me about a man of letters who made a habit of learning a new word every day.  I don't remember who that was; I'm sure there's a lot of people who have made such a resolution over the years.

But it struck me that I don't need to make the effort, because I encounter at least one new word every day.  If nothing else, in my readings on history, science, evolution and genetics.  It wouldn't be hard to document just one per day, and it would oblige me to properly find out what it meant.

However, the exercise is not without its pitfalls - not the least of which is the interruption in the flow of reading, the communication of information.  Not trivial when I'm deeply immersed in a train of thought.  Jump off that train, make a note, catch it again, recapture the meaning and the mood.  Later, I have to fit in the time to do the research and write it up.  Not always trivial.  In fact, since I started this, I realise I have a bad habit of glossing over new or half-understood words.  I find I'm not picking up half the candidate words - there's just too many.  In general, I'll try to make them totally new.

And so the second question: Why something as staid as ungulate?

Well, there will be days like that.  For some of these words, I didn't know the full meaning or nuance; for others, it makes sense to be clear on the understanding of a word that's needed for another word.  Like this one.

Ungulate

Do you know properly what this word means?

Of course, an ungulate is effectively a hoofed animal, but the word refers to a specific grouping of mammals. They move on the tips of their toes, which have hooves. (they'd be good at ballet, hey?)

There are odd- and even-toed ungulates, which actually delineates which toes the animals rest their weight on (some of the toes are quite vestigal, and so barely visible).

Despite what wikipedia says in its intro, this is not a proper cladistic group of animals. That is, the word does not describe a grouping of a single ancestral animal and all its descendants. Otherwise, you'd have to call dolphins and other cetaceans ungulates, because some ungulates are closer in ancestry to cetaceans than they are to other ungulates.

So this word is not very helpful scientifically - despite which, I'm sure some biologists use it informally to communicate meaning to a general audience.

  Where did I (last) encounter this word? I found it integral to the next word of the day - it helps to understand this one first.

Gravity and the narrow confines of life

Life on Earth has evolved within a very fine set of parameters.  We are going to find it a challenge to survive outside the sheltering cocoon of this planet, not the least because our atmosphere protects us from several types of radiation, not the least from our friendly sun.

Now there's another limitation.

Our body's physiological processes are to a great extent governed through the triggering of gene expression, which generates proteins that affect metabolic pathways of chemical reactions.  Translated, this means chemical signals trigger the unwrapping and copying of genes (sections of our DNA blueprint) that in turn generate proteins that... make our body work.

For that to happen, amongst other things we need... gravity.

On the one hand, one might intuit that gravity shouldn't be an essential part of our processes.  But we are generally pulled in a single direction: towards Earth, the largest mass at hand.  From an evolutionary perspective, that amount of gravity is an intrinsic part of the environment in which so many successive iterations (generations) successfully mutated and survived.  Our environment tempered the direction of successful mutation.

So it makes sense that our metabolic processes could be so finely tuned that significant change (ie, to zero gravity) could disrupt some of these processes.

And that's what's been found, as reported in New Scientist this week (4 February 2012).  Specifically: "weightless conditions... could disrupt the activity of 200 genes linked with immunity, metabolism and heat tolerance."

There is a slight caveat on that: the study used flies, and simulated weightlessness through magnetic fields.  Still, the researchers are confident of their results, it sounds plausible, and doubtless the result will be tested by others in other experimental contexts.

Still, just as science can bring the science fiction of space travel crashing to Earth, surely technological solutions will be developed.  After all, science fiction has already imagined simulated gravity.  It just hasn't filled in the details.

Irrational decision-making as evolutionary survival

One of the key fallacies of orthodox economics is that people are rational decision-makers with perfect information.

We can knock "perfect information" in so many ways, but a recent New Scientist article* reminded me how irrational we are, too.

Inter alia, the article points out something quite meaningful: that we have "a brain shaped by natural selection to see us through this messy world".

Think about that.  Although survival-wise it helps to be capable of rational thought (and all that goes with it, such as thinking ahead, concept-of-self, etc), that doesn't ipso facto mean that our brains evolved in the unitary direction of rationality only.  That's a very good explanation for an awful lot of human foibles.



Some examples of decision-making factors we probably inherit in an evolutionary sense are: existing biases, emotions, expectations, co-operation and conformity (sometimes you just follow the herd).  Altruism too: the article suggests that the consequent feel-good is "evolution's reward to team players".

A good example of irrationality in decisionmaking: discounting the future: the strong preference for small gains in the present over large gains in the more distant future.  This is a great factor in the sub-optimal global response to environmental threats.

Some of the not-entirely-rational mechanisms mentioned by the article include:

- confirmation bias: our propensity to be taken in by something that confirms our pre-existing biases;
 - loss aversion: it feels worse to lose something small than to risk it to gain something large;
 - the anchoring effect: basing decisions in novel situations on random, loose, or irrelevant connections;
 - the sunk-cose fallacy: deciding whether to continue [expending resources] on the basis of what's already been put in it (a common trap for many investors and poker players alike);
 - inconsistent preferences: preferring a over b, b over c, but c over a.

For the last one, it is suggested that we are likely to be making choices based on several different factors that may be decided by different areas of the brain, so ultimately "your preference will depend on the region that dominates at the time" - that is, when you are faced with such a binary decision.

At various times, these "tricks" can all be seen as useful survival mechanisms - and sometimes this means survival in a group sense rather than individual.

so it's noto necessarily a problem: it's just that as individuals we're not as rational as we'd like to think.

And the article says we face between 2,500 and 10,000 decisions every day.  Daunting, if we didn't use short cuts.

*"Making Your Mind Up" by Kate Douglas in the 12 November 2011 issue.  Oh all right, it's not recent, but I'm a bit behind, and I only just unsealed it recently.

Frogs and hybrid fungi

A few days ago I posited that humans are affecting ecosystems globally on a scale that rivals extinction events in the distant past.

Subsequent to that I unsealed an old copy of New Scientist that I'd been saving for a rainy day.  The 12 November 2011 issue mentioned  a disease that is "decimating frogs around the planet."

The cause is a fungus lethal to frogs called Batrachochytrium dentdrobatidis.  Sixteen of the 20 samples collected globally were a genetically identical strain (called BdGPL), ie they were of the same origin.  And they are "extremely virulent."

That strain was clearly a hybrid, formed in the past 100 years, most likely due to the "20th-century pet and food trade", which enabled the strains to meet.

Madagascar and south-east Asia are the regions most at risk right now, being "hotspots of amphibian diversity" and free of this fungus right now.

Globalisation is an inevitable process in the development of human society.  Such collateral damage need not be inevitable, but it takes political will which in turn, at the very least, would entail using one's vote wisely.

wildcats and cows: the manufactured world

Experience with animal husbandry was a significant influence in the ready and rapid acceptance of evolutionary theory when Darwin finally published On The Origin Of Species in 1859.

There has been long centuries of practice in breeding animals, selecting for a given trait (such as placidity) and deselecting for the undesirable. Aggressive cows ended up on the table along with the passive ones, but their genes don't get propagated thorugh breeding stock.

Result: walking larders.  Humans have, over the centuries and millennia, had such an influence on plants and animals that on the one hand as foodstock, the current versions of wheat, cows, and most else, is nothing like the original wild plant or animal - and indeed in many cases the wild original no longer exists.

On the other hand, humans have reduced most dangerous predators to either extinction, isolation, or simply governable.

There's a Scottish wildcat still in existence.  It's actually a local remnant of the European wildcat Felis silvestris silvestris - which was inimical to human activity, and so was hunted down over the centuries. Not to extinction, as it happens, but not for want of trying. The larger ones were killed; only the smaller ones got away. Thus artificial selection over time resulted in a wildcat that was not much bigger than the domestic cat, and often mistaken for one.

These two examples illustrate the push and the pull that humans are exerting on the world's fauna: reducing it to either the manageable or the usable - or, with the destruction of wildlife habitat, the ignored.

Climate change is only one side of the anthropisation of the planet:  the spread of human culture has already massively shifted the world's DNA stock.  Globalisation brings an attendant spread of uniform food habits and farming practices - amd is shifting the balance still further.  To push the world's DNA in a very specific direction - to greater uniformity in that which serves humans, is surely making our biosphere less robust to trauma.  The bee colony collapse disorder will be seen as an archetype for that degradation of biodiversity.  The cause doesn't need to be directly human, but the planetary changes that allow problems to become global has only one cause.

Dicynodont fossil find is evidence of... what?

How meaningful were media reports (eg  in the UK Telegraph, The Age) in December of a dicynodont fossil find in Tasmania?

The find, dated back to about 250 million years ago, was reported in the Journal of Vertebrate Paleontology, but interested-party scientists and media have a strong interest in making the information a story.  Thus overlaying a slant and significance that the lay person cannot easily navigate.

Dicynodonts (I’m told it’s pronounced dee-, not die-, which does not sound palatable to me, but that probably shows what an amateur I am) were widespread both before and after the great Permian extinction 245 million years ago (which marks the start of the Mesozoic era, typified as the “age of the dinosaurs”).  That event wiped out 80% of animal species and is still subject to debate over cause, although volcanic activity is a popular explanation.

But these animals survived.  They’re not just a single species really, but an infraorder: a group of species one below a class (such as mammals).  They were herbivores, ranging from small to cow-size, the “most successful and abundant land vertebrates of the late Permian” period, according to Wikipedia.

And after an extinction such as the Permian, the various environments are largely depopulated, and ripe for expansion by any species that can survive.  And in fact, after the Permian, a single subset of the dicynodont – the lystrosaurus genus, comprising about five species – truly proliferated throughout the world.  However, the world at the time of the lystrosaurus – and the dicynodont found in Tasmania – was very different – it was one big continent, referred to as Pangea.  Spreading wide would not be a problem at that time – if a species was suitably adaptive to the environment.

So the Tasmania find was not even narrowed down to a species, and it’s not surprising to find it in Tasmania, which was part of Australia until recently, and thus part of Pangea.

In fact, another dicynodont fossil had previously been found in Australia - announced in 2003, after re-examination of a fossil held for decades in Queensland Museum.

Dicynodonts are part of a wider grouping of animals called therapsids, of which only mammals remain.  Yes, all dicynodonts and descendants eventually became extinct.

And despite one of the interested-party scientists (Andrew Rozefelds) saying that the find “fills an important gap in our knowledge of these mammal-like reptiles and where they lived”, I’m still struggling to find what gap it fills.  It’s not to be found in the media.  Alas, access to the Journal of Vertebrate Paleontology is by subscription only.  Maybe if I get to a university library sometime…

References

ABC Science: Ozfossils

Tudge, Colin (2000): The Variety of Life, OUP

Wikipedia: including dicynodont, lystrosaurus, therapsid, permian

Evolution and monotremes, spam and off-topic Google searches

This post will discuss monotremes in evolution, but first a diversion to the reason for this topic.

I got a comment submitted from "Izumu":

"Hi Stephen,
I am Izumi from TBS TV, a Japanese TV company. We are intersted in the platypus egg photo you posted on your blog of 19 Mar 2008. I couldn't find your email address and that's why I'm making comment trying to be in touch with you. Could you kindly write me back to xxxxx@nifty.com ? Please don't post my comment since it includes my email address. Thank you very much for your coopereation. Izumi "

I post a reproduction of this comment sans email address, although I was inclined to include it anyway.

I get quite a number of spam comments posted, which is why comments are moderated.  I'm not inclined to reply to this request directly, because:
a) It was off topic;
b) The email address wasn't from an official TBS domain - Nifty is just a Japanese ISP.

Usually I just mark spam as spam.  I don't usually get a comment that's so close to falling either way.


There's a few pictures of platypus eggs on the web.  As it happens, mine is now at the top of Google Images.  It was a bit of a tragedy in some ways, because the actual topic of the post was the evolution of milk, but it gets caught in the wrong net.  If you want to communicate about platypus eggs, talk to someone who's communicating about platypus eggs.

The reason they appear to us to be strange is just a quirk of evolution: they are the last representatives of the earliest types of mammal.  The only egg-laying mammals (protherians) left are the monotremes, two species of echidna (porcupine-like creatures) and one of platypus, all native to Australia/Papua New Guinea.  Yet the first mammals were egg-layers.  Marsupials (metatherians: live but under-developed birth) and then placentals (eutherians: live birth) were a much more recent development, as the technology of birth evolved over tens of millions of years.

The oddness of the platypus may initially be due to their appearance, including webbed feet and a duck-like bill.  The fact that  they're mammals that lay eggs draws people in more.  But they are distinctive for two more reasons: they have poisonous spurs on their ankles (which seem to be for breeding purposes!), and they hunt through muddy water by sensing electrical fields.

The platypus, in evolutionary terms, is not so odd.  Pretty much all these features have evolved separately in other animals.  That's evolution: the time spans involved are so vast that if mutation can produce a lasting feature once, it can do it again.

No, the true oddness of the platypus lies in its survival to a time where most of its features are seen as uncommon.  There's a warning there: the survival of features that do not catch on (radiate) more broadly - in numbers or variety - is more indicative of desparately clinging to a vanishing niche than of evolutionary success.

The future of this blog [genetics 000]

It has come to my attention that...
I know I've been a bit slack lately...
There is so much richness in this world that there's never enough time to explore it all, let alone diarise it...

Ideally, I'd write a thought a day; heaven knows there is an abundance of fresh insights to be gleaned from the experiences of each and every day.  On the other hand, there's a putative obligation to pursue the insight to the full extent of its value, else why even start?

So, the world is still turning, new experiences are daily deposited in the bank of life's richness.  Where is the reward in not sharing it?

Time, that is the villain.  It seems to accelerate, leaving me guilty and struggling in its wake.

Not that I've been idle.  But as it stands, the less time I spend commuting, the less I have to devote to absorbing and recording.  (In any case, my commuting time had been taken up with podcasted lectures.)


To date, evolution constitutes the majority of my [tagged] posts.  Not surprising; it's been a fascinating journey - unexpected, and very rewarding.  But I've taken an equally fascinating, equally unexpected turn: to molecular biology and genetics.

Although the confluences could be mapped, this path certainly wasn't planned.  And I'm not a gadfly, turning to a new subject at whim.  In fact, before dipping into evolution, I'd not plunged so deeply into an area of study outside a formal university course.  And I had hitherto treated biology as the distant, neglected cousin of all the sciences, steeped as I had been in mathematics and physics.



A starting point could be: "what is a gene?"  Actually, I have attempted this in the past, with understandably mixed results.  So I felt I should not start the recording process until I'd got that under wraps.  Yet by the time I felt sufficiently confident, I'd come out the other end, and in fact discovered where within this wide area my true temperament and interest lies.

I will not start with the above question - the answer is not sufficiently straightforward.  I will start at the natural starting point: the basics of molecular biology.

It's not dry and uninteresting.  It's a fascinating universe writ small, and it touches on many of my core concerns, including information science, analysis, evolution, mathematics, and pure intrinsic beauty.


I will be trying to construct an engaging, coherent narrative.  Yet I will still take minor excursions into some of my traditional interests: music, film, current events, and science (first up will be a film called The Swimmer).

I even know exactly where this journey is taking me: genomics, wherein lies a universe of challenges - and which is one of the most current, most relevant worlds left to be explored.  For a hint of this, there's a truly inspiring lecture by Eric Lander of MIT, called Genomics (it's available for free on iTunes).  Although its clarity is worthy of the best of the visionary TED lectures, the full richness of its meaning will be far better appreciated with sufficient context.  That's what I'm aiming to provide.

Flores and toolmakers: Rethinking pre-sapiens hominid evolution

Science is uniquely accepting of new understanding, through new evidence.  (This is, of course, exploited by science deniers, who hide under the veneer of scepticism to push ideology over the balance of evidence.)  Yet most discoveries add to new knowledge, rather than shift paradigms.  Relativity and quantum physics are two of the few examples of abrupt change in the past 100 years.


There is good scientific consensus that the modern human species (Homo sapiens sapiens) first evolved in Africa, left about 60,000 years ago, and arrived in southeast Asia about 45,000 years ago.

However, other human species had left earlier: Homo erectus  first left Africa about 2 million years ago, spread widely, and was to be found as recently as 50,000 years ago in Java. (By contrast, Neanderthals, homo sapiens neanderthalensis, reached Europe between 600,000 and 350,000ya, lasting to 30,000ya.  Tellingly, sub-Safaran Africans have been found to have no Neanderthal DNA, while all other humans have 1-4% DNA from Neanderthals.)

Australopithecus afariensis and Homo floriensis (from Wikipedia)

More recently, the find of Homo floresiensis on the Indonesian island of Flores, has been dated to as recently as 13,000ya, going as far back as 94,000ya.  This is well before the emergence of modern humans, although evidence suggests the two species could have lived in close proximity for a time.

The H floresiensis remains are in fact so recent that they comprise original material, as opposed to fossils, which are rock which replaced (at a later point) eventually-disintegrating bone matter.

Because of the spread of H erectus, it has been speculated that this more recent find is descended from H erectus, and still underwent a dwarfism typically associated with animal species that have migrated to island environments.

Adam Brumm of the University of Wollongong reported recently in Nature  a find of tools in Wolo Sege in Flores that pushed back hominid (which is not to say H sapiens sapiens) occupation of Flores to at least 1,000,000ya.

Recently on ABC Radio, Brumm commented that the working hypothesis is that the tools belonged to an ancestor of H Floresiensis, since they were the only ones there that far back.  He also suggested that, rather than descending from H erectus, H floresiensis descended from an australopithecus species, so is hominid rather than human (Australopiths having evolved into the several homo species, and died out, about 2mya).

The important takehomes are that pre-hominids may have left Africa much earlier than hominds, and that H floresiensis is likely more distantly related to humans than any other homo species.  (Note: current thinking has chimpanzees diverging from humans about 5-6mya, which would put floresinensis divergence at 2-5mya.)
If Brumm's comments are correct, there may need to be a name change from H to A floresiensis.

This accords well with plenty of the other evidence on H floresiensis (albeit  floresiensis likely underwent further evolution apart from dwarfism).

Brumm called it an exciting time to be in the field, but also said they now needed new sedimentary basin finds [in Flores] to explore the period from 2mya to 1mya.  Despite the science, paleontology finds are still a matter of skilled luck as much as anything else.


Other references:
An ABC report on the tool finds;
anthropologist John Hawkes comments on the tool finds

Dawkins, religion, and some Australian politicians

There was an interesting panel discussion on tv last night: ABC's Q and A (subtitled Adventures In Democracy) - you can view the telecast at their website here.  The panellists were:

- Richard Dawkins, evolutionary biologist, currently visiting Australia;
- Julie Bishop, deputy leader of the (conservative) opposition;
- Steve Fielding, conservative independent MP who holds a critical balance of power position in the Senate;
- Tony Burke, Minister for Agriculture, Fisheries, and Forestry;
- Jacqueline Ninio, a (very!) liberal rabbi, not elderly but not young;
- professor Patrick McGorry, mental health expert and Australian of the Year.

Most of the discussions revolved around evolution (/creationism) and religious belief (/atheism).

Those discussions drew their basis in a series of questions from the studio audience (obviously hand-picked to cover a spectrum while having something to say) and live questions from the internet.

The results were surprising in some ways.

Richard Dawkins, very precise and learned, garnered the most frequent and the most sustained applause from the varied studio audience.  He was very cogent in his reasoning and insightful in his points.  Yet he was consistently maladept - almost autistic - in his people skills.  He claimed - quite wrongly - to be respecting other peoples' point of view, or right to hold that point of view.  He claimed a courtesy/respect that he didn't notice he wasn't paying.  Having said that, in other ways he did garner the most respect from the studio audience.

Jacqueline Ninio (rabbi) came across as particularly intelligent and thoughtful.  She went out of her way to respect alternative opinions, yet didn't come across as particulary wishy washy.  She had a religious leader's respect for religion, yet a real thinker's approach to comparative religion and philosophy.

Tony Burke (primary industries minister) was a surprise - to those who have not seen him in action (myself included).  He was a particularly practical, down-to-earth man, while showing a high level of thoughtfulness and intelligence - a bit like a farmer's temperament with a professor's thoughtfulness.  He very sharply pulled up Dawkins for the latter's ill-considered claim to respecting others' view.  Yet at the same time, he wouldn't have strongly disagreed with most of Dawkins' words - apart, maybe, from the strident atheism.

Patrick McGorry (professor of mental health) tried to - and succeeded in - avoiding controversy.  His most memorable contributions were when he was called upon for some thoughts on the mental health aspects of such topics as religion and asylum seekers.

Julie Bishop (deputy opposition leader) displayed intelligence, by and large.  On occasion she could be caught out falling back on her conservative, religious background.  But she was by no means the worst offender, who was...

Steve Fielding (independent - Family First - MP).  Let's face it: the bloke is a clown.  The only reason he is ever paid any attention to anywhere is because of his - accidental - pivotal role in federal politics.  On occasion he claims to have a science degree, but it was really engineering, and he displayed an appalling lack of interest in, or understanding of, science.  To make matters worse, he vascillated on pretty much everything.  He patently found himself an intellectual midget on the panel - and, no doubt, as compared to those in the studio audience. He persistently refused to tie himself down to any belief or understanding at all, and fell back on the "everybody has their right to..." mantra, especially when directly asked for his own views.  He professed to being a creationist, but when pressed as to whether or not he was a young earth creationist (ie the world is less than ten thousand years old), his evasion suggested he hadn't even thought about it.

As a visitor and internationally the most well-known of the panel, Dawkins was obviously the centre of attention for the evening - not because he intentionally monopolised the conversation, but because he was called upon for comment so much - to the point, in fact, that much of the discussion was reaction to his comments.

Yet it was particularly worthwhile to hear the contributions of Burke and Nunio, both of whom consistently instilled levelheadedness to the discussions.

Conversely, Fielding was the comic relief; the only way he could have avoided that would have been to refuse to say anything.

It's worth listening to the whole of the discussion, to gain insight into those people, those topics, and in particular how different people approach those issues differently.

Life on Earth is indeed a rare contingency

New Scientist reports that cosmic radiation would be too dangerous for NASA to send people to Mars.

NASA's current rules on risk aim to keep each astronaut's lifetime risk of radiation cancer to below 3%.  That limit would be reached in under 200 days, but a round trip to Mars would take 750 days.

Read the report here.


It would be relatively easy to shield a spacecraft from the sun's radiation.  But galactic cosmic radiation, comprising "protons and heavier atomic nuclei" has higher energy than the sun's, and can cut through DNA in living cells, which damage can lead to cancer.  On Earth, we are protected from such bombardment by both atmosphere and the Earth's magnetic field.

It does seem that the particular set of circumstances that fostered evolution and maintains life on Earth is a rare contingency, requiring the right combination of atmosphere, magnetic field, distance from the sun, type of sun and type of planet - even plate techtonics contributes to the ongoing habitability of the planet.

The piling up of such factors could help explain the lack of success in the Search for Extra Terrestrial Intelligence project.  It remains inconceivable that those factors could not arise repeatedly elesewhere, but the very delicacy of balance of all these factors is a plausible explanation for why we have fould no near neighbours.

Postscript 20-Oct-09: I have come across two memes that claim to speak to this.  First, the Drake Equation, which purports to estimate the number of civilizations in our galaxy (the Milky Way) with which we could establish contact.  Seven factors are included, including the rate of star formation and  the proportion of life-potential planets that go on to develop life.  A current estimate of the solution to that equation is 2.31; however, the equation (and estimates of factors) must be seen as so conjectural that to my mind it's little more than a philosophical exercise (or something akin to economists being asked to estimate something they know very well they don't have enough information for).

There is also a claim that there are "20 factors" necessary for the emergence of life with the complexity that we know.  However, I have not found the origin for this meme, and it's debated more in circles religious (both Christian and Muslim) than logic, scientific, or mathematical - invariably to "prove" the small contingency of life.  Still, there are necessary factors, and they're worth considering - albeit some of them surely overlap in terms of contingency.  For the purposes of debate, some of those mentioned include:
 - a liquid iron planetary core (to provide a magnetic field that shields us from some cosmic radiation);
 - a moon to pull tides (and circulate oceans) - (how necessary?);
 - the sun's composition;
 - the planet's distance from the sun;
 - distance from the centre of the galaxy... etc.
A scientific enumeration (and discussion) of such a list would be interesting to read (factors in Drake's equation are rather more broad - and conjectural - than these).

Yet I'd have to point out that at least some of these factors only pertain to our version of life.  It is hard for us conceive of life emerging in radically different form (and I'm not talking SF bugs or tentacled aliens: more, different formations of cells, etc), but that doesn't mean it can't happen.

Cormorants, and the evolution of birds

I thought the bird I saw on Coogee beach was somewhat duck-like in size and shape - except that it held its chest high, and had a sharp beak and rather large webbed feet.  Obviously a fisher.  It was entirely black (including feet), save yellow markings around the eyes.

It was actually a Great Cormorant (Phalacrocorax carbo), a widespread native to Australia.

Birds are most closely related to crocodilians, in the dinosaur clade archosauromorpha.  (Reptiles, thus, are paraphyletic - not really a true, complete evolutionary grouping, and rather just a description).

But let's take it from the top.  Or, at least, the beginning of the mesozoic (the "middle", or dinosaur era of 250 - 65 million years ago).  Archeosaurs (the precursor group to archosauromorphs) arguably became more successful at the time than synapsids (mammal ancestors) because they were better suited to the dryness of the Triassic period (250 - 200mya).  They included dinosaurs, crocodilians, and the ancestors of birds.  Crocodilians first appeared about 84mya (late Cretaceous).  Modern birds (neornithes: feathers, no teeth, hard eggs, several flight adaptions) evolved into a variety of forms in the Cretaceous (145-65mya).  The two bird groupings, palaognathae (comprising ratites - most of the flightless birds - plus the barely-flying tinamous) and neognathae (the rest) probably arose before the KT meteor event of 65mya, but radiated into the numerous different species mostly afterwards.

Now, the reason that cormorant looked a bit duck-like to me was its webbed feet and the shape and size of its body.  But they are not related at all.  Cormorants have been grouped together as pelecaniformes (which includes the pelican's family pelicanidae), while ducks are in the anseriforme order.

Although Colin Tudge (in The Variety Of Life) is happy enough with the cormorant's above classification, Wikipedia casts doubt on pelecaniformes being a true clade (that is, a single complete evolutionary grouping), and suggests phalacrocoraciformes as a more properly monophyletic clade.  The issue here is that the pelecaniforme was used to encompass all birds with fully four webbed toes.  But as we know, classification based on such a stark physical trait is dangerous, since the various species could easily have evolved separately but convergently.  If the purpose (webbed feet for paddling) is so clearly useful, that evolutionary change could have happened several times, several locations.

The names cormorant and shag are sometimes used interchangeably, but even when each is called by its proper name, there is no consistency between them.  Their collected family name is Phalacrocoracidae - but the discussion there concludes that this is not one consistent evolutionary grouping.

The cormorant I encountered was not well, if it was so near humans.  It was wandering around, not flying, and unlike the one above had most of its tail feathers missing - and appeared far too tame for its own good.  It and kids were a danger to each other.  I contacted the wildlife rescue organisation WIRES, who recommended taking it to a vet that was on the Wires register; so I took it to Struggletown in Randwick.  Unfortunately, it died within the next two days - as a result of lead poisoning.  How?  Unknown, and this was not the first bird specimen to be sent off for analysis for this issue.  Also not known what the missing tailfeathers had to do with its plight.  I was told the apparent tameness was due to lack of interaction with humans.  Still, it was the indirect effect of human activity that got it in the end.

Is evolution still happening?

Every so often, someone lands on my site specifically because they're wondering this: is evolution still happening?

Depends what you mean, really.  We hear often how viruses and bacteria mutate, seeming to generate new ways to attack us all the time.  Take bacteria (which are more readily classed as living entities).  They proliferate by dividing (binary fission), and their generations are far, far more rapid than ours.  Greater population, fast breeding, more scope for genetic change that is more visible to us.

Yet broadly we conceive evolution in terms of how we humans got to where we are today.  And that's the product of hundreds of millions of years (and elaborated in my earlier discussion here).  Saying that is one thing, but understanding it is far more difficult, because our human scale takes its measure in one lifetime.  At best, we extend ourselves to the whole of human history, which is only a few thousand years - a tiny speck on the scale of hundreds of millions.  I call this issue deanthropocentrism: the effort required to conceptually escape our human framework, and understand processes that work on vastly different scales.  To do this more than superficially is not nearly as easy as it sounds.

So some of us think, how can this be, does this evolution really make sense?  Yes, it does, just not so much in our immediate framework.

Yet the sun is still emitting radiation that occasionally knocks around with DNA in our germ-line cells, producing the odd change.  Such changes can add up over time, if beneficial for survival.  If a mutation improves the odds of an individual surviving and breeding, that mutation is more likely to survive.  In the past, this was "natural selection" - ie, mutation survived where the "whole of environment" (including climate, food resources, food competitors, and predators) fostered it.  These days, humans frequently take that role, exercising selectivity over both plant and animal breeds.

How does selectivity work today on humans?  Well, we've diluted it substantially.  By improving global health, we're over-riding natural selectivity.  We're increasing the survival rates of those who have adverse genetic outcomes.  For example, cystic fibrosis sufferers once seldom lived far beyond puberty, but survival has now been prolonged past breeding age.

Is that a bad thing?

No, because we are ethical beings, not ones to ride on the whim of random outcomes.

Over time, our technology can improve outcomes, identify potential issues before they happen, find solutions.


And we are now at the point where the environment is a product of us, not vice versa.  So what of climate change?  Although we can say human adaptions that are better suited to a hotter, more turbulent world are better able to survive, the question is whether those less adaptive are likely to survive to breed.  And our global culture no longer fosters selectivity purely on that basis - bar a calamitous breakdown of society.

So these are the issues: whether and how we intervene in 'natural' selectivity.  Such intervention can bring human evolution to a halt.  The only selectivity for breeding now is societal, and I have seen no indication so far of any specific genetic determinant on those who end up remaining single all their lives (in the sense that they produce no offspring).

In that sense it could be said that humans, for the time being, have induced their own evolutionary pause.  However, that might not be such a bad thing: natural selectivity could work in any direction, depending on environment.  Bigger (or brighter, or more complex) is not necessarily better for survival, for example - as the dinosaurs found out.

Cambrian explained: early multicellular animals

The trifecta of interest in early evolution is: the emergence of eukaryotes (cells with nuclei), multicellularity, and animals.

There are signs of life at 3.8 billion years ago, just 700 million years after the formation of the Earth. I've discussed in more detail the advent of eukaryotic life here. The discussion below revolves around multicellular animals, and several discoveries that push back the timeline of their emergence. This ameliorates the picture of Cambrian-period "explosive" evolution, and replaces it with a more steady narrative. As in all paleontological tales, the evolution of understanding is a matter of both further discovery, and finer interpretation of existing evidence.

The first multicellular life (algae) dates back 1 billion years; the first multicellular animals date from 575 million years ago (the sponge-like Ediacarans).

From 542 to 520 million years ago in the Cambrian period was the relatively sudden evolution of more modern animal forms, which has piqued the curiosity of many, including Stephen Jay Gould. Gould explains the difference between Ediacaran animals and modern ones in terms of body layers: the former are diploblastic while the latter are triploblastic, essentially meaning they have an outer layer (ectoderm), a gut (endoderm) and, most importantly, a mesoderm in the middle, which lends the capacity for complex internal organs.


Traditionally, as a central narrative of animal evolution, the Cambrian explosion lacked context. However, more recent discoveries place the ancestors of Cambrian animals much further back, to about 850 million years.

One discovery concerns analysis of the bountiful Doushantuo Formation, a seabed fossil lode from China. Dating from 550 to 580 million years - latter times for the Ediacarans - tiny spheres have been found to be early animal embryos. Hard, spiky shells ruled them out as large bacteria, and those same shells, sans embryo, have been identified from 632 million years, early Ediacaran period.


This finding was reported in 1998 (Xaio, Zhang, and Knoll in Nature), and discussed at length by Gould in Lying Stones Of Marrakesh (notwithstanding his continued maintenance of special significance he previously accorded to the Cambrian).

Going back further, to 635-713 million years ago, a form of cholesterol has been found, 4-isopropylcholestane, now found only in some sponges.

Further: 850 million year old rocks in Canada (MacKenzie Mountains), which contain stromatolites (traces of cyanobacteria), have also been found to have a particular pattern of calcium carbonate which has been identified as characteristic of a collagen mesh, which only animals build. The discoverer (Canadian Elizabeth Turner) says the life form was even more primitive than a sponge: "a few different types of cells living together in a shared, collagenous matrix".

These discoveries fit well with molecular clock calculations: that is, comparative DNA analysis had already put back the advent of animals to about this time frame - yet evidential traces hadn't been identified until now. Others cast doubt on the interpretations of the evidence above, while still accepting animal evolution as dating back further than other evidence has shown.

I think a key aspect of the emergence of multicellular animals is the environmental backdrop. Photosynthetic bacteria started producing oxygen about 2.5 billion years ago, although this did not extend beyond a few metres of the ocean surface. This oxygen had been poisonous to most life to that point, but fostered development of oxygen-tolerating life. Atmospheric oxygen propelled a chain of circumstances resulted in the lower reaches of the ocean being not just anoxic, but also laden with hydrogen sulphide. Although some bacteria thrived in these conditions, the combinations would have been a "persistent brake on eukaryotice evolution" (according to the above Andrew Knoll).

Then came the second "snowball Earth" ice age, which was seen to "reset the chemistry of the oceans" to make life more favourable to multicellular animal forms. Yet conditions at first were more conducive to smaller, soft-bodied organisms - which, over time, changed the balance, perhaps by eating inimicable bacteria. On one interpretation, increased oxygenation was a result rather than a cause of animal evolution - although it makes more sense that they worked in tandem. The same is conjectured for the set of ice ages that occurred around that time: they could have been just as much a consequence of animal evolution (by sucking out carbon when buried) as a cause. It's easy to envisage a slowly oscillating set of equilibria that eventually settled to a higher oxygen, animal-rich, warm Earth - especially as there were no more snowball Earths once larger animals had evolved (notwithstanding subsequent ice ages of smaller scale).

A fascinating narrative, and one that is more appealing than sudden bursts of evolutionary activity. More detail in the New Scientist article below.


References
Gould, SJ (2000): Of Embryos and Ancestors in Lying Stones Of Marrakesh, Vintage, London.
Fox, D & Le Page, M (2009): Dawn of the animals in New Scientist, 2009, 11 July.