Dr. Ann Gauger has a short post at Evolution News about a new paper in the peer-reviewed journal BIO-Complexity.
Winston Ewert of Biologic Institute has just published a new article in the peer-reviewed journal BIO-Complexity (“Overabundant mutations help potentiate evolution: The effect of biologically realistic mutation rates on computer models of evolution”).
He and his colleagues have been engaged in a series of critiques of evolutionary algorithms for the last several years.
[…]The advantage of these computer simulations is that they can be run many, many times and thus approximate the long time necessary for biological evolution. The disadvantage is that they do not replicate true biological evolutionary processes, but use “analogous” algorithms. Typically these models, such as Ev and Avida, are purported to solve complex problems.
Yet Ewert and his colleagues have shown that in every case the necessary information for the models to find their targets was smuggled in, whether intentionally or not, by the respective programmers.
[…]Ewert shows that even taking the models as they are, when they are tested using realistic scenarios they fail to accomplish their goals. In fact, they accomplish little beyond their starting positions. He determines the reason for this failure — the models can only go as far as one step will take them. They can’t evolve anything that requires two or more mutations, unless mutation rates are unrealistically high.
Here’s the abstract of the new paper:
Various existing computer models of evolution attempt to demonstrate the efficacy of Darwinian evolution by solving simple problems. These typically use per-nucleotide (or nearest analogue) mutation rates orders of magnitude higher than biological rates. This paper compares models using typical rates for genetic algorithms with the same models using a realistic mutation rate. It finds that the models with the realistic mutation rates lose the ability to solve the simple problems. This is shown to be the result of the difficulty of evolving mutations that only provide a benefit in combination with other mutations.
This reminds me of William Dembski’s “No Free Lunch” theorems, which show that you can never get information for free, through simple mechanisms like genetic algorithms. The only proven source of functional information is an intelligent agent.
The Earth’s Atmospheric Conditions Are Favorable to Life:
The surface gravity of Earth is critical to its ability to retain an atmosphere friendly to life. If Earth’s gravity were stronger, our atmosphere would contain too much methane and ammonia. If our planet’s gravity were weaker, Earth wouldn’t be able to retain enough water. As it is, Earth’s atmosphere has a finely calibrated ratio of oxygen to nitrogen—just enough carbon dioxide and adequate water vapor levels to promote advanced life, allow photosynthesis (without an excessive greenhouse effect), and to allow for sufficient rainfall.
Ok, that’s very good.
Now here is one from me… well, it’s from Science Daily, but I found it. Actually, ECM found it. But he told me.
They suggest that the size and location of an asteroid belt, shaped by the evolution of the Sun’s protoplanetary disk and by the gravitational influence of a nearby giant Jupiter-like planet, may determine whether complex life will evolve on an Earth-like planet.
This might sound surprising because asteroids are considered a nuisance due to their potential to impact Earth and trigger mass extinctions. But an emerging view proposes that asteroid collisions with planets may provide a boost to the birth and evolution of complex life.
Asteroids may have delivered water and organic compounds to the early Earth. According to the theory of punctuated equilibrium, occasional asteroid impacts might accelerate the rate of biological evolution by disrupting a planet’s environment to the point where species must try new adaptation strategies.
The astronomers based their conclusion on an analysis of theoretical models and archival observations of extrasolar Jupiter-sized planets and debris disks around young stars. “Our study shows that only a tiny fraction of planetary systems observed to date seem to have giant planets in the right location to produce an asteroid belt of the appropriate size, offering the potential for life on a nearby rocky planet,” said Martin, the study’s lead author. “Our study suggests that our solar system may be rather special.”
So, that’s 5 ways that the Earth and our solar system are fine-tuned to be habitable for complex, embodied minds. Somebody is looking out for you, so be thankful and recognize.
Actually, I was thinking about this today (Wednesday). At lunch, I was thinking about this girl I know who is very disrespectful of me, of what I’ve achieved, and she won’t take my advice in the areas where I am experienced – education, career, saving, investing. I was fretting about it as I was about to start eating my lunch and suddenly it struck me that I don’t give God enough credit for the many blessings I get from him. I don’t mean things that “go my way”, I mean big things like habitability, and so on. So I said a longer grace than normal today at lunch. I wonder if he sent me that rebellious girl so that I would know how he feels when I don’t recognize and respect him, and just complain about the things he doesn’t do for me.
Anyway, I hope this habitability post will give you something to be thankful for. Our God is an awesome God.
The paper was published in the Quarterly Review of Biology. I found it on PubMed.
Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.
By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?
After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:
It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)
Behe argues that this point is empirically supported by the research reviews in the paper. He writes:
As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported
After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:
Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.
But this stark lack of examples of gain-of-functional coding elements can have important implications:
A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.
Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.
I have read and listened and watched a lot of material on intelligent design, but I have never seen so much value packed into such a short lecture. I really hope you’ll watch this and that it’s helpful to you.
the big question when discussing the origin of life: where did the information in living systems come from?
Until 530 million years ago, the oceans were largely devoid of life
In a 10 million year period, many new forms of animal life emerged
New biological forms of life require new information
the discovery of DNA shows that living systems work because cells have information that allows them to build the components of molecular machines: cell types, proteins, etc.
can random mutation and natural selection create new functional information?
normally, random mutations tend to degrade the functionality of information, e.g. – randomly changing symbols in an applications code does not usually introduce useful new functions, it usually renders what is there non-functional
the majority of possible sequences will NOT have functions, so random mutations will more likely give you non-functional code, rather than functional code
example: a bicycle lock with 4 numbers has many possible sequences for the 4 numbers, and only one of them has unlock functionality, the rest have no functionality
if you have lots of time, then you might be able to guess the combination, but if the lock as has 10 billion numbers, and only one combination that unlocks, you can spend your whole life trying to unlock it and won’t succeed
how likely is it to arrive at a functional protein or gene by chance? Is it more like the 4-dial lock (can be done with lots of time) or the 10 billion dial lock (amount of time required exceeds the time available)?
the probability is LOW because there is only one sequence of numbers that has unlock function
consider a short protein of 150 amino acids has 10 to the 195th power possible sequences
if many of these sequences of amino acides had biological function, then it might be easier to get to one by random mutation and selection than it is with a lock that only unlocks for ONE sequence
how many of the possible sequences have biological function?
Thanks to research done by Douglas Axe, we now know that the number of functional amino acid sequences for even a short protein is incredibly small…
Axe found that the odds of getting a functional sequence of amino acids that will fold and have biological function is 1 in 10 to the 77th power
Is that number too improbable to reach by chance? well, there are 10 to 65th atoms in the entire Milky Way galaxy… so yes, this is a very improbable outcome
can random genetic mutations search through all the sequences in order to find the one in 10 to the 77th power one that has biological function? It depends on how much guessers we have and how many guesses we get in the time available
even with the entire 3.5 billion year history of life on Earth, only about 10 to the 40th organisms have ever lived, which far smaller fraction of the 10 to the 77th total sequences
even with a very fast mutation rate, you would not be able to reach a functional protein even with all that time, and even with all those organisms
I was once having a discussion with a woman about the research that Axe did at the Cambridge University lab. He published four articles in the Journal of Molecular Biology. I held out one of the papers to her and showed her the numbers. She said over and over “I hate the Discovery Institute! I hate the Discovery Institute!” Well, yeah, but you can’t make the Journal of Molecular Biology go away with hating the Discovery Institute. JMB is peer-reviewed, and this was experimental evidence – not a theory, not a hypothesis.
We have been blessed by the Creator and Designer of the universe in this time and place with overwhelming evidence – an abundance of riches. For those who have an open mind, this is what you’ve been waiting for to make your decision. For the naturalists who struggle so mightily to block out the progress of experimental science, they’ll need to shout louder and shut their eyes tighter and push harder to block their ears. Maybe if they keep screaming “Star Trek” and “Star Wars” over and over to themselves, they will be able to ignore the real science a little longer.
Access Research Network is a group that produces recordings of lectures and debates related to intelligent design. I noticed that on their Youtube channel they are releasing some of their older lectures and debates for FREE. So I decided to write a summary of one that I really like on the Cambrian explosion. This lecture features Dr. Stephen C. Meyer and Dr. Marcus Ross.
The lecture is about two hours. There are really nice slides with lots of illustrations to help you understand what the speakers are saying, even if you are not a scientist.
Here is a summary of the lecture from ARN:
The Cambrian explosion is a term often heard in origins debates, but seldom completely understood by the non-specialist. This lecture by Meyer and Ross is one of the best overviews available on the topic and clearly presents in verbal and pictorial summary the latest fossil data (including the recent finds from Chengjiang China). This lecture is based on a paper recently published by Meyer, Ross, Nelson and Chien “The Cambrian Explosion: Biology’s Big Bang” in Darwinism, Design and Public Education(2003, Michigan State University Press). This 80-page article includes 127 references and the book includes two additional appendices with 63 references documenting the current state of knowledge on the Cambrian explosion data.
The term Cambrian explosion describes the geologically sudden appearance of animals in the fossil record during the Cambrian period of geologic time. During this event, at least nineteen, and perhaps as many as thirty-five (of forty total) phyla made their first appearance on earth. Phyla constitute the highest biological categories in the animal kingdom, with each phylum exhibiting a unique architecture, blueprint, or structural body plan. The word explosion is used to communicate that fact that these life forms appear in an exceedingly narrow window of geologic time (no more than 5 million years). If the standard earth’s history is represented as a 100 yard football field, the Cambrian explosion would represent a four inch section of that field.
For a majority of earth’s life forms to appear so abruptly is completely contrary to the predictions of Neo-Darwinian and Punctuated Equilibrium evolutionary theory, including:
the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phylum-level body plans;
small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and
a steady increase in the morphological distance between organic forms over time and, consequently, an overall steady increase in the number of phyla over time (taking into account factors such as extinction).
After reviewing how the evidence is completely contrary to evolutionary predictions, Meyer and Ross address three common objections: 1) the artifact hypothesis: Is the Cambrian explosion real?; 2) The Vendian Radiation (a late pre-Cambrian multicellular organism); and 3) the deep divergence hypothesis.
Finally Meyer and Ross argue why design is a better scientific explanation for the Cambrian explosion. They argue that this is not an argument from ignorance, but rather the best explanation of the evidence from our knowledge base of the world. We find in the fossil record distinctive features or hallmarks of designed systems, including:
a quantum or discontinuous increase in specified complexity or information
a top-down pattern of scale diversity
the persistence of structural (or “morphological”) disparities between separate organizational systems; and
the discrete or novel organizational body plans
When we encounter objects that manifest any of these several features and we know how they arose, we invariably find that a purposeful agent or intelligent designer played a causal role in their origin.
Recorded April 24, 2004. Approximately 2 hours including audience Q&A.
You can get a DVD of the lecture and other great lectures from Access Research Network. I recommend their origin of life lectures – I have watched the ones with Dean Kenyon and Charles Thaxton probably a dozen times each. Speaking as an engineer, you never get tired of seeing engineering principles applied to questions like the origin of life.