On the Evolution of a Novel Function

Published on 5 March 2019 in The Proceedings of the National Academy of Sciences of the United States of America:

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids

Xuan Zhuang, Chun Yang, Katherine R. Murphy, and C.-H. Christina Cheng

You can read the article here: https://www.pnas.org/content/116/10/4400

The authors show how an apparently irreduciblly complex phenotypical element arose by a combination of mutation and natural selection.

“The Ascent of Man”, Forty Years On

In the late 1960’s, the British Broadcasting Corporation commissioned Jacob Bronowski to prepare a television series entitled “The Ascent of Man”. Apparently, the series was meant to be a scientific bookend to Kenneth, Baron Clark of Saltwood in the County of Kent OM CH KCB FBA’s “Civilisation” series, which was an historian’s view of how we ended up where we are.

Bronowski’s series aired across the world (and even this benighted high-school student watched it gobsmacked in Brisbane, Australia). Bronowski died in 1974, not long after the series was published. He also wrote a “book of the series”, which came out in 1973 (it is one of my treasured possessions, moth-eaten as it is).

A brief biography:

Jacob Bronowski was born in 1908 into a Jewish family in the Polish city of Lodz. His parents moved to Britain in 1920 and Bronowski pursued his senior studies in mathematics at Cambridge University. He later studied and conducted research in physics. He taught at the University College of Hull during the 1930s. During the Second World War, he conducted research on the effectiveness of Allied bombing campaigns, culminating in being part of a British Government survey of the results of the attack by the United States on Hiroshima and Nagasaki. As a result of his experiences in Japan, he turned from physics to biology to try to understand the nature of violence in humans.

His subsequent career includes many writings on what knowledge means: he concerned himself with the epistemological question of “what can we reliably know?”. The Ascent of Man series seems to have been his attempt to answer this question.

(I may have his history wrong, in which case, I apologise).

If you wish to see what he said in the series, fragments of the Ascent of Man series are available on Youtube via a search for “Bronowski Ascent of Man”.

My question is this:

Now, after forty years, how much did Bronowski get right?

My personal view is that Bronowski is mostly right. My version of his argument is that we construct useful knowledge out of a combination of imagination and observation. Science is philosophy (what can be) constrained by evidence (what is).

I am interested to know what this community thinks about Bronowski’s work, with the benefit of forty years of hindsight.

(my thanks to Gregory for alerting me to my misattribution of the “Civilisation” series to Sir Arthur C Clarke CBE FRAS).

The ID explanation is too easy to vary

I like David Deutsch’s description of explanations (I think it comes from him): a good explanation is hard to vary.

An explanation says that some particular settings of claimed causes best explain some observed pattern in nature.

An explanation is likely to be good if other settings of the proposed causes predict a different pattern from what we observe – it is hard to vary the settings and still explain things as they actually are.

To make it concrete, a particular setting of gravity (acceleration of 32 feet/sec/sec) at the surface of the Earth explains the pattern we see when apples fall off trees. Any other setting of gravity would not yield the pattern we actually observe. The explanation is hard to vary and still explain the observed results.

An explanation is likely to be bad if a wide range of settings of the cause(s) can be chosen and the resulting pattern remains the same.

The basic argument of intelligent design is that there is a cause (the Intelligent Designer) for the observed pattern of life. Any number of other, subsidiary causes may be involved, but it is impossible for the diversity of life to have arisen without the intervention of an intelligent designer.

How should we assess this explanation? Look at the settings. As Daniel Dennett advises, twiddle with the causal knobs. What do we find in the intelligent design explanation?

Continue reading

On The Origin of Species, read by Richard Dawkins (2007)

There is grandeur in this view of life, with its several powers having been originally breathed into a few forms or into one, and that while this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning, endless forms most beautiful and most wonderful have been, and are being, evolved.

These are the closing words of Darwin’s On the Origin of Species, read abridged in an audio recording by Richard Dawkins from 2007.

How should we read Darwin’s book today?

Should we read it as history? Is On The Origin of Species a Hopeful Monster of a theory lacking a mechanism and made irrelevant by more recent discoveries?

As politics? Is the book no more than a privileged English gentleman naturalist explaining interesting but unsupportable things to his own social class?

As science? Is it no more than a naturalist’s attempt to synthesise what was known or speculated from biology, geology and paleontology, physics and chemistry as it was known at the time?

Continue reading

ID, ENCODE and the Happy Isles of Fitness

As Neil Rickert was foolish enough to grant me posting rights, I had better take advantage of the offer before the sysops sensibly change their minds.

Consider an argument used consistently by the ID community: that the natural processes of genetic mutation and environmental selection acting upon the resultant variation are incapable of generating speciation.

Their recurring metaphor is of improbable islands of fitness separated by unbridgeable seas of non-functionality. Even if the hill-climbing capability of “random mutation plus natural selection” is real (and even incorporating unselected allele frequency changes), evolution can’t work because “you can’t get there from here”. For brevity, let me acronymise this argument as CANTSWIM.

CANTSWIM has a great many shortcomings as a metaphor for how evolutionary processes actually work, and you don’t need me to enumerate them. But let me hand over the title deeds to the evolutionary farm, and assume that CANTSWIM is factual.

At the same time, the ID community has adopted the claim made by the leadership of the ENCODE program that >80 per cent of the human genome is functional. The devil, of course, is in the detail of how “functional” is defined.

Continue reading