Tag Archives: Complexity

Podcasts

Ann Gauger’s new peer-reviewed paper on Darwinian evolution

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Amazing new research paper by the Biologic Institute. The PDF of the paper, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” is available here.

The MP3 file is here.

Participants

  • Jay Richards, Director of Research at the CRSC, (Discovery Institute)
  • Ann Gauger, senior research scientist at the Biologic Institute

About Ann:

Ann is a senior research scientist at Biologic Institute. Her work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry.

Topics:

  • Co-authored with microbiologist Ralph Seelke at the University of Wisconsion
  • Purpose: study whether bacteria can evolve the ability to fix a broken protein (e.g. – enzyme)
  • Two areas are broken in the enzyme
  • If you fix the first one, it works a little but not fully (slight advantage)
  • If you fix the second one, it starts to work fully (huge advantage)
  • It’s a “two-step adaptive path” – a textbook case for evolution
  • should be able to hit both mutations and get back full functionality
  • At the start of the experiment, the cell is churning out broken protein
  • there is a cost to the cell for create the broken protein
  • the cell can either go through the adaptive path and repair the protein
  • OR, it can shut off production of the broken protein
  • EITHER PATH gives a selective advantage
  • So what happens? The cells NEVER followed the adaptive path
  • They almost ALWAYS turn off the production of the broken protein
  • It happens in 30-50 generations, in 14 different cultures
  • Each culture had a different way of turning off the production
  • They tested on 10^12 cells
  • Only one cell made the first repair, none made the second repair
  • It’s more advantageous to STOP PRODUCING the broken protein as soon as possible
  • The first cell that gets rid of the non-functional protein first overtakes the whole culture
  • so, even adaptive paths that provide a benefit with one mutation are unlikely to be followed
  • The point: even promising theoretical adaptive pathways MAY NOT WORK in experiments

I wrote about Doug Axe’s recent research paper here. He is the Director of the Biologic Institute.

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Podcasts

Doug Axe publishes a new peer-reviewed paper on protein folding

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A new podcast from ID the Future is worth listening to.

Participants

  • Jay Richards, Director of Research at the CRSC, (Discovery Institute)
  • Doug Axe, Director of the Biologic Institute

The MP3 file is here.

Topics

  • the new BIO-Complexity peer-reviewed journal
  • new peer-reviewed paper challenges Darwinian account of protein folding
  • proteins are found in every living system
  • a protein is a chain of parts called amino acids
  • there are 20 amino acids used in living systems
  • it’s like a 20-letter alphabet used to make sentences (proteins)
  • if the sequence is just right, it folds up and has a function
  • the information about the functional sequences is in the genome
  • the “protein fold” is the 3D shape that a functional protein takes on
  • the folding problem is good because you can TEST Darwinian mechanisms
  • the problem is simple enough to be tested rigorously in a lab
  • Question: how easy is it to create a sequence that folds?
  • English is a good analogy to the problem of protein folding
  • you have a long string of characters (e.g. – 200 letters)
  • each “letter” can be one of 20 amino acids
  • if you assign the letters randomly, you almost always get gibberish
  • there are tons of possible sequences of different letters
  • it’s like a 200 digit slot machine with each digit having 20 possibilities!
  • the number of sequences that would actually make sense is tiny
  • protein folding is the same
  • Doug’s paper assesses how many “tries” could have been attempted
  • Doug’s paper calculates the total number of possibilities
  • cells have arrived a large number of functional sequences
  • but only a small number of the total possibilities could have been tried
  • this is called the “sampling problem”
  • there isn’t enough time to test all of the possibilities (see previous paper below)
  • how did living systems arrive at the functional sequences so quickly?
  • there are some possible naturalistic scenarios for solving the problem
  • Doug’s new paper shows that none of the naturalistic explanations work
  • the only explanation left is that an intelligence sequenced the amino acids
  • it is identical to the way that I can sequence letters to make this post

A picture is worth a thousand words

Here’s a video clip from the DVD Darwin’s Dilemma showing the process:

If you would like to know more about Darwin’s Dilemma, you can read Brian Auten’s review of Darwin’s Dilemma.

Who are these guys?

I wrote a post before on Doug Axe’s previous publications in the Journal of Molecular Biology, where he researched how many of the possible sequences of amino acids have biological function. His PhD is from Caltech, and his post-doctoral research on proteins was conducted at Cambridge University.

Jay Richards is a Senior Fellow of the Discovery Institute and a Contributing Editor of The American at the American Enterprise Institute. In recent years he has been a Visiting Fellow at the Heritage Foundation, and a Research Fellow and Director of Acton Media at the Acton Institute. His PhD is from Princeton University.

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Polemics

How long will it take to sort a deck of cards by trial and error?

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Inside the cell, things like proteins and DNA are formed by sequencing parts together in just the right way so that the sequence will have biological function. If the sequence is wrong, because some component of the sequence is the wrong piece or is in the wrong place, the sequence has no function. It’s just like writing English or computer instructions.

To calculate the probabilities, you have to use a rule called “The Product Rule”, because the order of the parts in the sequence (“permutation”) is important. For example, the odds of getting the sequence “ABC” just by choosing three random letters is 1/26 x 1/26 x 1/26 = 1/17576. Things get very unlikely quite quickly, don’t they?

So, take a look at Neil Simpson’s latest post, where he uses cards instead of letters or amino acids, but the principle is exactly the same. His calculation is a little different because the odds actually go down a little each time you choose a card. So, for the first card, it’s 1/52, but the second card is only 1/51, and so on…

Excerpt:

This is by no means a definitive argument against evolution, but I offer it to put the “time, chance and random mutation” theory in perspective.

Everyone knows that micro-evolution occurs, such as dog breeding and bacteria becoming resistant to antibiotics.  But macro-evolutionists believe that with enough time an amazingly complex single cell of unknown origin could make lots and lots of small changes, develop reproductive capacities and eventually become humans, elephants, caterpillar/butterflies, chameleons and so much more.

Let’s consider something very simple.  Imagine that you shuffle a deck of cards.  If you shuffled it one time per second, how often would all the cards go back into their original order? (Ace of spades, King of spades, etc.)  The math is simply 1/52 (the odds of the Ace of spades being on top) times 1/51 times 1/50, etc. I left out the Jokers to make it easier.

Guess how many years it takes?

Click through to see his calculations, or do them yourself! It’s easy and fun! Neil has a pretty fun discussion going on with the angry atheists who frequent his site, too.

This is everyone should learn probabilities in school, because then we can really talk about these things with our neighbor. Shalini can even do biochemistry, so she can actually explain it even better than I can!

Remember, we are looking for a specific sequence of cards – the sequence that the cards originally came in. In this example, it’s that sequence and that sequence alone that has biological function. The other sequences are just junk – they have no biological function. And most importantly, you don’t get to save any of the cards that are in the right spots because the sequence as a whole has no present function that would allow it to be “saved” for later. You have to re-select all 52 cards each time at random!

A typical protein isn’t made of 52 parts, it’s made of around 200, and there are 80 possible amino acids, not just 26! And in the case of proteins,the vast majority of the possible sequences that you can make won’t have any biological function at all! (And there are many more problems besides, such as chirality, cross reactions, and bonding type). Even if you filled the whole universe with reactants and reacted it all at Planck time, for the entire history of the universe, you still wouldn’t be likely to get even one protein!

You can read more about the origin of life in this post.