Since there’s been some discussion on new body plans, here is my understanding of how they come about. Note that I am not a biologist. I’m sure someone will correct me if I am wrong. Most of this has to do with how branching processes work.

To explore how new body plans arise, we are going to travel back in time with my trusty time machine. I obviously don’t have a time machine, which is why this is only a thought experiment. As I travel back in time, I take along a passenger, whom I shall call “William”. We want to find out where the octopuses, with an obviously different body plan, arose.

We start our journey in the present, looking at a person — perhaps at William himself. Then we go back in time to look at the ancestors. Well go fast, or this would take for ever.

As we go back in time examining ancestors, we see earlier vertebrates, such as fish. We keep on going, and get to the early chordates. They had a neural bundle, but no vertebrae. We have to go further back to find the ancestors of the octopus. As we go back, we see ancestors without even a neural bundle. Eventually, we get back to the point where the ancestors of the octopus branched off.

At this point, we see two sibling organisms. One of those is an early ancestor of us, and the other is an early ancestor of the modern octopus.

I hand William a microscope, and ask him to examine both as closely as possible, and to describe the body plan that he can see in each. “What body plan” says William. “I don’t see any body plan.”

That’s where the phylum branching occurred. The body plans came later. The whole idea of “macro-evolution”, as that term is used by creationists and ID proponents, is just a complete misunderstanding.

Man has created many sophisticated modelling tools, all of which have different strengths and weaknesses. A good ‘solution’ or ‘description’ of a problem should not be overly complex (parsimony) and also have high descriptive power. Let’s look at how some of these cutting edge tools compare to Nutonian‘s symbolic regression / evolutionary computation product Eureqa:

from: http://blog.nutonian.com/bid/330675/How-does-Eureqa-Compare-to-Other-Machine-Learning-Methods#!

Looks like we get highly efficient yet incredibly accurate models. Huzzah! Don’t believe me? try it yourself. They “ran Eureqa on seven test-cases for which data is publically available, and compared performance to four standard machine learning methods. The implementations used were the WEKA codes, with settings optimized for best performance”. Weka is free and the Eureqa trial version is free.

Enjoy the full post here

Unfortunately I think Hod’s interpretation of NFL isn’t quite there, though. 😉

Recent posts by Sal remind me that there are some intelligent educated people who doubt Common Descent.  What I don’t understand what they think the alternative is. Put simply I take Common Descent as the position that :

* At one time there was only very simple unicellular life on earth (this is not a debate about how that unicellular life originated)

* Complex life forms (eukaryotes) are created by slight modifications from other life forms (which are their parents). We have never observed them being created any other way!

* All complex life forms are the descended from a very small number of simple life forms – quite possibly just one.

The alternatives I can imagine are:

* Complex life descended many different times from simple life forms – so e.g. mammals descended from a different simple life form from fish. This flies in the face of the fossil record and the hierarchical nature of complex life but I can sort of understand it.

* Complex life from time to time gives birth to wholly different species – massively implausible.

* Complex life is created anew by some process never imagined or observed – even more implausible but presumably what Young Earth creationists believe.

But maybe there is another option?

If Sal or someone could explain I would be interested.

[cross posted at UD: The Blind Watchbreaker would dispose of lunches even if they were free — mootness of anti-NFL arguments]

Our colleague Elizabeth Liddle has described the process of human design as trial and error, tinkering and iteration. Like Dawkins, she has argued nature (like human designers) is able to construct biological designs via trial and error, tinkering and iteration. However, when nature is properly compared and contrasted with the way humans go about creating designs, it is apparent Dawkins’ claim of a blind watchmaker is false.

I refer to Elizabeth’s description because she articulated some aspects of the blind watchmaker hypothesis better than Dawkins, but in so doing actually helped highlight why Dawkins’ blind watchmaker is refuted by the evidence.

[this is a follow up post to Selection falsely called a mechanism when it should be called an outcome]
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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?

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Denis Noble has a new review out, in Experimental Physiology called Physiology is rocking the foundations of evolutionary biology.  Unfortunately the article itself is behind a paywall, but here is the abstract:

The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection. Any role of physiological function in influencing genetic inheritance was excluded. The organism became a mere carrier of the real objects of selection, its genes. We now know that genetic change is far from random and often not gradual. Molecular genetics and genome sequencing have deconstructed this unnecessarily restrictive view of evolution in a way that reintroduces physiological function and interactions with the environment as factors influencing the speed and nature of inherited change. Acquired characteristics can be inherited, and in a few but growing number of cases that inheritance has now been shown to be robust for many generations. The 21st century can look forward to a new synthesis that will reintegrate physiology with evolutionary biology.

It’s a nice synthesis of the views he expresses in his book, The Music of Life, which I mentioned a previous post, Reductionism Redux , but he also lays out very clearly the ways in which four assumptions that have underlain much thinking in evolutionary biology since the “modern synthesis” (not so modern now), need to be revisited.

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as Per Ahlberg bills it at Talk Rational:

Boisvert, C. A., Joss, J. M. P. & Ahlberg, P. E. 2013: Comparative pelvic development of the axolotl (Ambystoma mexicanum) and the Australian lungfish (Neoceratodus forsteri): conservation and innovation across the fish-tetrapod transition. EvoDevo 4: 3.

The paper is open access, available here. Abstract:

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