Free Online Course: Introduction to Genetics and Evolution

I think the light moths tasted better. I think that's why the birds ate them. And any self-respecting bird population would have evolved better eyesight so they could see the dark moths better. That way they could eat more and live longer and leave more offspring. Mung

Mung posted this:

So they were choosing to eat light moths rather than dark moths?

You are getting close, but are still fixated with the teleological thing. The birds selectively eat the light-coloured variant on dark-coloured trees because they are easier to see. The melanised moths enjoy a reproductive advantage as a result. Once the industrially induced darkening of the trees is reversed, the selective pressure of predation moves to the variant that is more obvious. timothya

timothya:

In the early, smoggy phase the lichens die off revealing the light coloured moth variant.

Well, surely the lichens evolved too then.

No design required. Just natural selection doing what it does.

Natural selection does not do anything. You evidently understand how natural selection actually works. Saying natural selection works implies a force of some kind. Natural selection does not "work," it is not a "force." It's not a cause, it's an effect. Oh, look, more dark moths! If that's what you guys mean when you say evolution is true, grats to you. If you went around killing light colored moths I'd call that selection.

Predators selectively pick them off...

So they were choosing to eat light moths rather than dark moths? Mung

Mung posted this:

It doesn’t take a genius to figure out if you have a population of light and dark colored moths and you kill off more light colored moths that the relative numbers of dark colored moths will increase, and vice versa

The only mistake you make is in the use of ther term "you" (there is no conscious "you" involved). In the case of the peppered moth, the "killing off" was done by the blind, impersonal pressure of the environment that the moths lived in. In the early, smoggy phase the lichens die off revealing the light coloured moth variant. Predators selectively pick them off, so the population moves inexorably towards an average dark colour. After the Clean Air Act, and the concomitant reduction in industrial pollution, the light coloured lichens return. The predator species find the dark variant easier to locate, and the selective pressure of the environment changes the moth colour allele in lockstep. No design required. Just natural selection doing what it does. Little steps, my friends, little steps. You evidently understand how natural selection actually works. Now ask the next question . . . (Meanwhile avoiding the pitfall of claiming more than you know) timothya

timothya, It doesn't take a genius to figure out if you have a population of light and dark colored moths and you kill off more light colored moths that the relative numbers of dark colored moths will increase, and vice versa. If that's what you guys mean when you say evolution is true, grats to you. Mung

Eric Anderson posted this:

I was frankly astounded — 20 years after Philip Johnson’s disection of the peppered moth story the example of evolution in action that was used by the good professor was, you guessed it, the peppered moth story.

Could you (for my benefit, if not for anyone else) explain your astonishment by providing a brief summary of the salient features of Johnson's rebuttal, and why you think those features remain valid today? A few dot points covering the headland arguments would help me. I have read The Wedge of Truth and I am assuming that the book contains the dissection to which you refer. I am seeking to understand whether and why you think Johnson's arguments still stand. timothya

Ah, PaV, you're just too skeptical. Don't you know that any change over time from generation to generation is 'evolution' in action? Why, just today in our very first day of class we were reminded of this by the good professor. I was frankly astounded -- 20 years after Philip Johnson's disection of the peppered moth story the example of evolution in action that was used by the good professor was, you guessed it, the peppered moth story. BTW, he seems to be a very likeable guy and I think this will be an interesting course if we can manage to survive the scheduled indoctrination of the first week (evolution is a mathematical certainty; only dupes dispute it; there is no debate in the scientific community; etc.). I hope the thought police don't track me down . . . :) Eric Anderson

Genomicus:

However, when I say “species,” I typically mean a population of organisms capable of producing fertile offspring.

I'm currently reading The Beak of the Finch by Jonathan Weiner. We find out that the "Grants," working with the Galapagos finches on the island of Daphnea, could isolate 'seven' different species of ground finches. But, then, surprisingly, out of nowhere, two of the finches produced full-fertile hybrids. And, not only that, but the hybrids are increasing at a much higher rate than the crossed species. So they're "really" fertile. But, wait a second, this is a hybrid from 'two' of the 'species.' Per your definition, this looks like we don't have 'seven' species, but perhaps only 'six'. Or is it even fewer. But, taxonomically, these 'species' are considered separate 'species.' So, when you say that Darwinian processes can bring about new species, how can that be so given we have such a hard problem deciding what does, or does not, constitute a new 'species'? And, should I mention that the untrained eye couldn't tell the difference between any of these supposed 'seven' species, yet, I have no problem at all telling a Poodle from a Dalmatian, which are considered the SAME species. What a mess. In the end, I don't know how we can be justified in saying that RM+NS has brought about new and separate 'species', while freely admitting that, indeed, there are separate 'species.' BTW, Weiner's book is a really good read, full of very interesting information, and gives a great overview of "evolution in action." However, a careful read of it leads one to clearly see that Darwinian mechanisms have nothing at all to do with 'speciation.' It's a great book for disproving Darwinian evolution---contrary to the author's purpose. Genomicus, we'll just have to disagree on all of this. PaV

PaV:

At long last: what constitutes a ‘species’?

That's a good question, but unfortunately there is no truly rigorous definition of what constitutes a species. However, when I say "species," I typically mean a population of organisms capable of producing fertile offspring. Genomicus

Jonathan M, having recently completed your master's in evolutionary biology (congrats BTW), what's your purpose in taking this course? JoeCoder

Genomicus:

No. Allele frequencies of particular genes can differ within a species.

At long last: what constitutes a 'species'? PaV

Genomicus @52: Yeah, OK, I know the graph you are talking about. And I remember thinking when I hit that page that he was giving away the store. After all, he had spent the whole book demonstrating that even in a massive population with huge selection pressure you would only get a small handful of nucleotide substitutions, possibly only 2 or 3. But we have to remember that he was trying to establsh an absolute boundry and wasn't willing to put species outside that boundry. (I'm not sure I would be either, particularly given the rather fluid definition of species in particular circumstances.) Also, Behe doesn't state that all species can result from RM+NS, just that it is possible that some species could. Thus, I think I understand where you are coming from. But rather than saying that Behe thinks RM+NS "is perfectly capable of giving rise to new species" we should say something more along the lines of: "Behe doesn't dispute the possibility of RM+NS producing new species under certain circumstances." Eric Anderson

Genomicus, I would be interested in a statement from Behe that RM+NS can result in new species. That is very different from my understanding of his position.

Well IIRC, if you take a look at one of the figures in The Edge of Evolution,you'll find that Michael Behe suggests that the edge of evolution lies between species and class (with some ambiguity there). Which means that species are within the limits of non-teleological evolutionary processes. I don't have a clear idea of this figure because I read the EoE from a library copy, so I don't have it with me. Genomicus

PaV:

Does this mean their “allele frequencies” are identical?

No. Allele frequencies of particular genes can differ within a species. Genomicus

Genomicus: I hope you reply to my last post. I suspected that we would see things differently when it came to what constitutes a species. We're very close to discovering where we differ, so I hope the conversation can continue. PaV

Jonathan, could I suggest that the Intelligent Design scholars make an effort to produce a video course. Some of us live off these types of courses, but www.thegreatcourses.com for example have no Intelligent Design friendly courses that we know of. Christian-apologetics.org

Genomicus, I would be interested in a statement from Behe that RM+NS can result in new species. That is very different from my understanding of his position. Eric Anderson

Genomicus:

St. Bernard: Canis lupus familiaris. Chihuahua: Canis lupus familiaris.

Does this mean their "allele frequencies" are identical? PaV

PaV:

Are Chihuahuas and St. Bernards different “species”?

It doesn't look like it: St. Bernard: Canis lupus familiaris. Chihuahua: Canis lupus familiaris. Genomicus

Genomicus:

In agreement with Professor Behe, and others, I am suggesting that random mutation coupled to natural selection is perfectly capable of giving rise to new species.

Are Chihuahuas and St. Bernards different "species"? PaV

Hmm he recommends Jerry Coyne? He's not very fair nor open minded. See an expose of him here in one incident: http://jerrycoyne.blogspot.co.uk/2012/10/jerry-coyne-and-open-mindedness.html suyuti

This site is a goldmine. Thanks a lot, im gonna try the epigenetics course too! MaxAug

That is very interesting, Genomicus - especially, 'new to the field.' It is odd though that it should tend (my impression is, 'very pronouncedly), to be the young. I hadn't spotted, 'very young', which seems yet more remarkable. The more so, perhaps, in the light of a remark of the atomic physicist, Oppenheimer, which seems to bear on the subject: 'There are children playing in the streets who could solve some of my top problems in physics, because they have modes of sensory perception that I lost long ago.' That latter point, his explanation, is also interesting in terms of the course of the mundane course of our lives. I believe our brain routinely prioritizes the retention of what we remember and what skills we have learnt, according to our present needs, in terms of the more recent course of our lives. I believe that was why an Australain woman said to me anxiously that, when she thought of the work she had been doing as an accounts manager with an oil company, it kind of scared her, as she couldn't imagine being able to do it now - evidently fearing a pathological (if modest, in the scheme of things) loss of her cognitive powers. But she presumably, feared the loss was due to some medical, demential condition. Also, if you spread out a pack of cards, or an appreciable number of them, on a table - there is a game in which this takes place, a young child will normally, I believe, have a far better memory of the location of the cards. It was certainly the case with a young cousin of mine. But then, are not young children the truest of intellectuals, motivated purely by a desire to learn, to know. The world and its pressures and exigencies has not yet affected their outlook. They want to learn everything, on a far more undiscriminating basis than we. Axel

G:

In agreement with Professor Behe, and others, I am suggesting that random mutation coupled to natural selection is perfectly capable of giving rise to new species.

But taht doesn't mean anything wrt biological complexity. Joe

Damn, I was really hoping this course had evidence of macro evolution, who is arguing about micro? I don't think anybody on the planet denies adaptations.... Andre

Axel: I concur. To quote from Thomas Kuhn: "Almost always the men who achieve these fundamental inventions of a new paradigm have been either very young or very new to the field whose paradigm they change." Genomicus

'It’s not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.' I don't think so, JoeCoder. Max Planck summed it up all too epigrammaticaly: 'Science advances, one funeral at a time.' The teacher - assuming the youngster is correct - rightly feels his status is threatened, doesn't he? Your point is really tangential, indeed, another issue. It all hinges on who is correct. Nobody likes a smart Alec. Sure. But on such an occasion, the truth may dwarf personal feelings. Einstein was apparently a cocky student. Axel

to highlight the monumental problem that Darwinian processes face in generating fundamentally new species (as opposed to a new sub-species of a already existent parent kind): to reiterate:

"The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")

And yet, Dr. Behe, on the important Table 7.1 on page 143 of Edge Of Evolution, finds that a typical cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites in a multicellular creature is,,,

Largest-Ever Map of Plant Protein Interactions - July 2011 Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker. http://www.sciencedaily.com/releases/2011/07/110728144936.htm

So taking into account that they only covered 2%, of the full protein-protein "interactome", then that gives us a number, for different protein-protein interactions, of 310,000. Thus, from my very rough 'back of the envelope' calculations, we find that this is at least 30 times higher than Dr. Behe's estimate of 10,000 different protein-protein binding sites for a typical single cell (Page 143; Edge of Evolution; Behe). Therefore, at least at first glance from my rough calculations, it certainly seems to be a gargantuan step that evolution must somehow make, by purely unguided processes, to go from a single cell to a multi-cellular creature. Moreover, there is, 'surprisingly', found to be 'rather low' conservation of Domain-Domain Interactions occurring in Protein-Protein interactions between different species:

A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,, http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005096

Thus Genomicus, whatever you may have imagined for the ease of Darwinian processes to give rise to new species,,,

In agreement with Professor Behe, and others, I am suggesting that random mutation coupled to natural selection is perfectly capable of giving rise to new species.

,,, the fact of the matter is that Dr. Behe's work, despite what you may have imagined it to suggest, is completely antagonistic to the belief that RM and NS can do as such! As well, Dr. Behe's empirical research, that had found extreme difficulty for Darwinian processes to create just two binding sites, agrees with the extreme difficulty that is found for scientists trying to purposely design just a single protein-protein binding site:

Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011 Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required: "...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2" If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely? In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick! http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012 Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder. http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.html

Further notes:

Two Domain Protein - video (several binding sites required) http://www.facebook.com/photo.php?v=421708024519477 Why Proteins (Protein Domains) Aren't Easily Recombined - Ann Gauger - May 2012 Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification. http://www.biologicinstitute.org/post/22595615671/why-proteins-arent-easily-recombined "Why Proteins Aren't Easily Recombined, Part 2" - Ann Gauger - May 2012 Excerpt: "So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required." http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2

Verse and music:

Psalm 104:24 O Lord, how manifold are your works! In wisdom you have made them all. The earth is full of Your possessions Evanescence - The Other Side (Lyric Video) http://www.youtube.com/watch?v=HiIvtRg7-Lc

bornagain77

as to:

In agreement with Professor Behe, and others, I am suggesting that random mutation coupled to natural selection is perfectly capable of giving rise to new species.

And yet even though Dr. Behe may give far more credence to the supposed (contrived) evidence for common descent than is warranted, the fact is that, whatever views Dr. Behe personally has on common descent, he, in his book Edge of Evolution, adamantly does not hold that the mechanism of 'random mutation coupled to natural selection is perfectly capable of giving rise to new species':

The Edge Of Evolution - Michael Behe - Video Lecture http://www.c-spanvideo.org/program/199326-1 A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have "invented" little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution "Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use." http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge.html

In fact, Dr. Behe puts the 'edge of evolution' somewhere between species and class:

Behe comes to the conclusion that the edge of Darwinian evolution for a vertebrate lies somewhere between the level of species and class. That is, evolution cannot explain the categories above this level. Interestingly, creationist biologist Frank Marsh proposed in 1976 that the created kinds (baramins) were often at the level of genus or family, although sometimes at the level of order. (Figure 10.1, p. 218). http://creation.com/images/journal_of_creation/vol22/6472chart-lge.jpg

Dr. Behe states in The Edge of Evolution on page 135:

"Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite." "The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable." - Michael Behe - The Edge of Evolution - page 146

Dr. Behe's subsequent work has only further refined what he had originally found to the severe limitation of what random variation and natural selection could accomplish:

Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html Wheel of Fortune: New Work by Thornton's Group Supports Time-Asymmetric Dollo's Law - Michael Behe - October 5, 2011 Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection. http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html

The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

Out of the horse's mouth, Dr. Michael Behe talks about the preceding paper on this podcast:

Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

Thus, although Dr. Behe may support some form of common descent, he certainly does not think that Random Variation and Natural Selection are the main driving mechanisms behind common descent. bornagain77

Nevermind. I see now that the workload on the page is listed as 5-6 hours a week. JoeCoder

How much time each should I plan to devote to this course? JoeCoder

I’m presuming that you’re not in any way suggesting that this has been brought about by RM+NS. Correct?

In agreement with Professor Behe, and others, I am suggesting that random mutation coupled to natural selection is perfectly capable of giving rise to new species. Genomicus

Genomicus:

Therefore, the rise of a new species means the rise of a new form of biological complexity.

I'm presuming that you're not in any way suggesting that this has been brought about by RM+NS. Correct? PaV

Genomicus:

Species are regarded as complex (e.g., we’d all agree that elephants are complex creatures). Therefore, the rise of a new species means the rise of a new form of biological complexity.

New species can have the same form as the parent species. So it would all depend on how one defines "a new species" and "speciation". Joe

“Yes. Quoting passages of a theological nature is relevant to biological origins in which way, again?”

I guess you can ask God, who is the source of all life, when you see Him when you die.

That's not a scientific statement, though, is it? I mean, if I were to quote passages of the Koran, or the Vedas, or the Iliad and the Odyssey, or perhaps the Declaration of Independence - wouldn't you consider all that irrelevant to biological origins? Sure, they're interesting but really have no place in discussion about science IMHO. Genomicus

What is it you have in mind when you say this?

Species are regarded as complex (e.g., we'd all agree that elephants are complex creatures). Therefore, the rise of a new species means the rise of a new form of biological complexity. Genomicus

Joe Coder stated:

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student’s job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It’s not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

That's a agreeable 'play nice' long term strategy, but then again if you are, like me, a little like poor little Johnny (the butt of so many jokes) who is always raising his hand and asking questions and can't seem to keep from getting into trouble with the teacher in class, perhaps it would be good to have a little primer on where some of the major weaknesses of 'the overwhelming evidence for evolution' actually are?!!

Inherit the Spin: The NCSE Answers "Ten Questions to Ask Your Biology Teacher About Evolution" - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html (Not) Making the Grade: Recent Textbooks & Their Treatment of Evolution (Icons of Evolution update) podcast and paper - October 2011 http://www.idthefuture.com/2011/10/not_making_the_grade_recent_te.html

As to natural selection:

On Enzymes and Teleology - Dr. Ann Gauger - July 19, 2012 Excerpt: "This is an interesting turn in evolutionary thinking. People have been saying for years, "Of course evolution isn't random, it's directed by natural selection. It's not chance, it's chance and necessity." But in recent years the rhetoric has changed. Now evolution is constrained. Not all options are open, and natural selection is not the major player, it's the happenstance of genetic drift that drives change. But somehow it all happens anyway, and evolution gets the credit." http://www.evolutionnews.org/2012/07/on_enzymes_and062391.html Darwin’s Legacy - Donald R. Prothero - February 2012 Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. http://www.skeptic.com/eskeptic/12-02-15/#feature Austin Hughes: Most Evolutionary Literature Showing Positive Selection in the Genome is "Worthless" - Casey Luskin - 2012 Excerpt - When University of South Carolina evolutionary biologist Austin Hughes was asked about the problem with positive Darwinian selection, he says, "The problem is there really isn't all that much evidence that it actually happens to the extent to which it would be needed to explain all of the adaptive traits of organisms." http://www.evolutionnews.org/2012/01/austin_hughes_m055121.html Darwinism’s Last Stand? - Jonathan Wells Excerpt: Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best. Natural selection - like artificial selection - can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection - much less the origin of new organs and body plans. http://www.evolutionnews.org/2009/06/junk_dna_darwinisms_last_stand.html#more EXPELLED - Natural Selection And Genetic Mutations - video http://www.metacafe.com/watch/4036840 "...but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have..." Maciej Marian Giertych - Population Geneticist - member of the European Parliament - EXPELLED I got a new copy of ReMine’s The Biotic Message and re-read his chapters on Natural Seleciton and I get to see it all in action. (UD Blogger - Mung) Summary Inventive natural selection is the distinctive evolutionary mechanism – essential to Darwinian theory. Evolutionists presume it creates new adaptations by somehow traversing the hills and valleys of the fitness terrain. But they do not attempt to defend it as testable science. Rather, for the defense they shift back to the naive version – survival of the fittest. Then they might offer some tautology to help expunge all doubt. When challenged, they shift between various formulations They use naive natural selection to convince the public that evolution is simple, testable, and virtually inevitable. When opponents point out that such continually uphill evolution is refuted by the data, evolutionists effortlessly shift away from naive natural selection. Then they charge that the opponent has a poor understanding of evolutionary theory. In short, evolutionists merely shifted away from criticism, then focused their arguments (and your attention) in a direction that seemed to overcome the criticism. This phenomenon occurs at several levels. Biological adaptation by natural selection is not inevitable, nor is the theory scientific. It had merely lent support to the philosophy of naturalism. https://uncommondescent.com/intelligent-design/natural-selection-defies-the-odds/comment-page-1/#comment-384066 "Natural selection does not act on anything, nor does it select (for or against), force, maximize, create, modify, shape, operate, drive, favor, maintain, push, or adjust. Natural selection does nothing…. Having natural selection select is nifty because it excuses the necessity of talking about the actual causation of natural selection. Such talk was excusable for Charles Darwin, but inexcusable for evolutionists now. Creationists have discovered our empty “natural selection” language, and the “actions” of natural selection make huge, vulnerable targets." The Origin of Theoretical Population Genetics, 2001 (pp. 199-200) William Provine - Professor of Evolutionary Biology - Cornell University

bornagain77

Genomicus:

Speciation can be considered an example of new biological complexity.

What is it you have in mind when you say this? PaV

boragain77- If we have natural selection then we have evolution by Darwinian processes. That said natural selection doesn't do anything, so there would still be major issues for evolutionism. But anyway the course looks interesting and I am trying to set aside some time to take it. Joe

footnote:

The role of theology in current evolutionary reasoning - Paul A. Nelson - Biology and Philosophy, 1996, Volume 11, Number 4, Pages 493-517 Excerpt: Evolutionists have long contended that the organic world falls short of what one might expect from an omnipotent and benevolent creator. Yet many of the same scientists who argue theologically for evolution are committed to the philosophical doctrine of methodological naturalism, which maintains that theology has no place in science. Furthermore, the arguments themselves are problematical, employing concepts that cannot perform the work required of them, or resting on unsupported conjectures about suboptimality. Evolutionary theorists should reconsider both the arguments and the influence of Darwinian theological metaphysics on their understanding of evolution. http://www.springerlink.com/content/n3n5415037038134/?MUD=MP

bornagain77

Genomicus @16: I understand what you are saying and I agree the terminology is important. I also agree that a Darwinian process can account for some of what we see in the world: average beak size fluctuations in a population of finches; insects and insecticide (possibly); the malaria/sickle-cell example Behe reviewed in his book; the antifreeze [broken] protein in that Antarctic fish species; a few more examples along those lines. Interesting stuff to be sure; but in the broader context, pretty minimal stuff. My expectation is that the course will provide a good primer on genetics and also some decent examples of these microevolutionary changes we see. I agree with PaV that caveat emptor is in order as to the broader concept of "evolution" and any attempts that may be made to indoctrinate the student, particularly in light of the professor's recommendation of Coyne's book. In terms of terminology, part of my interest will be to watch the use of the word "evolution" and see when it shifts and changes meaning throughout the course (I would like to be polite and say "if" but I've had enough experience to know that it is not "if" but "when"). Will be interesting to see . . . Eric Anderson

ba77 @7: Interesting video. Started off slowly, but he did a decent job providing a description for the lay person. Unfortunately he went off the rails a bit at about minute 22 when he started trying to identify the designer . . . Eric Anderson

That’s not the only kind of biological complexity. Speciation can be considered an example of new biological complexity. A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter - July 2012 Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time. http://darwins-god.blogspot.com/2012/07/evolutionists-are-losing-ground-badly.html bornagain77

"Yes. Quoting passages of a theological nature is relevant to biological origins in which way, again?" I guess you can ask God, who is the source of all life, when you see Him when you die. As to, your theological concern, perhaps you could question Darwinists as to why they use predominantly theological arguments as a starting point, instead of reasoning to a theological end point as I did? The role of theology in current evolutionary reasoning http://www.springerlink.com/content/n3n5415037038134/ Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html From Philosopher to Science Writer: The Dissemination of Evolutionary Thought - May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html "One of the great ironies of the atheist mind is that no-one is more cock-sure of exactly what God is like, exactly what God would think, exactly what God would do, than the committed atheist. Of course he doesn’t believe in God, but if God did exist, he knows precisely what God would be like and how God would behave. Or so he thinks",,," Eric - UD Blogger bornagain77

Please fell free to cite just one novel functional protein arising by Darwinian processes.

(Note that I'm no Darwinian - I'm an ID proponent) That's not the only kind of biological complexity. Speciation can be considered an example of new biological complexity. Genomicus

Well, establishing if evolution by Darwinian processes is even possible IS the first step to take in ascertaining if you are on the right path scientifically, but once the crucial point is established that Darwinian processes are not even in the right ballpark as to being realistically plausible, then the supposed (read contrived) evidence for common descent proffered by Darwinists quickly falls apart upon closer inspection!

And the evidence for common descent explained by ID proponents like Prof. Behe, true? My point is this: if you're going to say that there is no evidence for evolution, you have to define what you mean. If you mean "common descent," then a lot of us around here will strongly disagree with you. Just saying, you know.

Darwinian processes completely fail to explain the origin of functional information and you wonder why ‘The Word’ (Logos) of John1:1 would be relevant???

Yes. Quoting passages of a theological nature is relevant to biological origins in which way, again? Genomicus

I’m pretty sure all of us ID proponents would agree that Darwinian evolution can account for some of the biological complexity in our world.

Please fell free to cite just one novel functional protein arising by Darwinian processes. bornagain77

Not all. any. difference

I'm pretty sure all of us ID proponents would agree that Darwinian evolution can account for some of the biological complexity in our world. Genomicus

Then you’re not asking for evidence of common descent

Well, establishing if evolution by Darwinian processes is even possible IS the first step to take in ascertaining if you are on the right path scientifically, but once the crucial point is established that Darwinian processes are not even in the right ballpark as to being realistically plausible, then the supposed (read contrived) evidence for common descent proffered by Darwinists quickly falls apart upon closer inspection!

or (asking for) evidence for evolution for that matter.

Au Contraire, I asking specifically for any evidence of 'vertical' evolution, i.e. of gain in functional complexity above what is already present!

Verse and music: Not meaning to be annoying, but what exactly does this have to do with the subject of intelligent design, Darwinian evolution, and biological origins as a whole?

Darwinian processes completely fail to explain the origin of functional information and you wonder why 'The Word' (Logos) of John1:1 would be relevant??? bornagain77

Genomicus:

You’re specifically asking for evidence that Neo-Darwinian processes can generate all the biological complexity we see today.

Not all. any. difference Mung

Evidence for evolution ‘in this context’? I don’t know, perhaps the same evidence I’ve been asking for for years?!? Perhaps, a single novel functional protein arrived at by purely neo-Darwianian processes??? or better yet a molecular machine arrived at by purely neo-Darwinian processes??? or perhaps best yet, a demonstration of the awesome power of evolution to create ‘layered transcription and overlapping coded programming’ within the genome that computer programmers can only dream of imitating?

Then you're not asking for evidence of common descent, or evidence for evolution for that matter. You're specifically asking for evidence that Neo-Darwinian processes can generate all the biological complexity we see today. I know it might seem like the semantics are unimportant, but we need to be careful to use the correct terms in the discussion over biological origins.

Verse and music:

Not meaning to be annoying, but what exactly does this have to do with the subject of intelligent design, Darwinian evolution, and biological origins as a whole? Genomicus

Further note:

Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description) http://vimeo.com/35088933

Verse and music:

John 1:1-5 1 In the beginning was the Word, and the Word was with God, and the Word was God. 2 He was with God in the beginning. 3 Through him all things were made; without him nothing was made that has been made. 4 In him was life, and that life was the light of all mankind. 5 The light shines in the darkness, and the darkness has not overcome it. Matt Maher - Hold Us Together (w. lyrics) -- music http://www.youtube.com/watch?v=Ut0ENzQcjrM

bornagain77

So what do you mean by “evolution” in this context?

Evidence for evolution 'in this context'? I don't know, perhaps the same evidence I've been asking for for years?!? Perhaps, a single novel functional protein arrived at by purely neo-Darwianian processes??? or better yet a molecular machine arrived at by purely neo-Darwinian processes??? or perhaps best yet, a demonstration of the awesome power of evolution to create 'layered transcription and overlapping coded programming' within the genome that computer programmers can only dream of imitating? notes:

Signature In The Cell - Review Excerpt: Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. http://www.fourmilab.ch/documents/reading_list/indices/book_726.html Evolution vs. Functional Proteins - Doug Axe - Video http://www.metacafe.com/watch/4018222 When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide "The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution") "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin http://www.metacafe.com/watch/8593991/ Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 Overlapping & Embedded Genes - video http://www.youtube.com/watch?v=mGnOQv76jcU Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html

bornagain77

Finally Jonathan, after all your studies, you finally made it to the top-secret hideout where Darwinists keep all their overwhelming empirical evidence for evolution that they keep telling us IDiots about but never producing for us!

Evidence for common descent is not the same thing as evidence for the view that "everything" in biology is the result of non-teleological processes. So what do you mean by "evolution" in this context? That said, there is a trace of a refreshing change going on among ID proponents. Slowly but surely, it seems like mainstream ID proponents are willing to actually learn about the theory that is being critiqued, and willing to critique the arguments made by other ID proponents (e.g., Sal's criticism of the 2nd law of thermodynamics.). Genomicus

Funny. One of the FAQ questions reads:

Does Prof. Mohamed Noor ALWAYS talk that fast? Yes.

I completed a small set of Google taught Python classes on youtube. If you can track this guys talking speed, Noor will be a a piece of cake: Google Python Class Day 2 Part 3 See if you can understand him on the first run. ;) If you are not familiar with any coding jargon you have a more difficult time. JGuy JGuy

PaV @4: No doubt you are correct. I notice he lists as part of the supplemental reading Coyne's Why Evolution Is True book. Looks like an interesting course, however, so with your caveat in place it might be worth checking out. Eric Anderson

Semi OT: I think Ian Juby does a excellent job in the following video, with one of the more complex subjects in the evolution vs. intelligent design debate, making the subject very accessible to the layman:

Thermodynamics & Information - Ian Juby - video http://www.youtube.com/watch?v=9dAA06Zfi4M

bornagain77

The evolution topics covered in the present course are largely confined to “microevolution,” though we hope to add some new topics spanning macroevolution to future course iterations.”

But macroevolution is just the result of repeated microevolution! Oh, wait! I thought creationists made up the micro/macro distinction. Mung

Perhaps those considering the course should note the following "The present version does not cover macroevolution or the diversity of life. There will not be anything about dinosaurs. The evolution topics covered in the present course are largely confined to "microevolution," though we hope to add some new topics spanning macroevolution to future course iterations." No doubt it will be quite interesting, but that seems to ignore a major area of concern. Isn't the question whether evolutionary processes, such as they are, have the POWER to drive speciation? Wasn't that the core of Behe's "Edge of Evolution?" Somebody help me out. Thanks Bruce Phillips

CAVEAT EMPTOR: There's nuts and bolts about biology; and, then, there's "evolution." That's the only part that concerns me. And what invariably you find, no matter what book you pick up, there is no way that they can use all the stuff they've told you about and then explain evolution to you. I've looked everywhere. Doesn't exist. So, if you want to learn "nuts and bolts" stuff, assuming you aren't already familiar, then this is a good class for you. But don't expect that in the end they will come up with an explanation for 'evolution' that even comes close to making any kind of sense. If you do, then you're just wasting your time. PaV

Thanks JM! And good point JoeC. I think I will sign up. Does this mean I can toss my "Evolution for Dummies" and "Complete Idiot's Guide to Evolution" books? Mung

Thanks for sharing. I've been looking for something exactly like this and will likely be signing up. Will anyone else? I think David Klinghoffer's A piece of Unsolicited Advice to Students may be appropriate to keep in mind:

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

JoeCoder

Topics that will be covered in this course include: Evidence for evolution

Finally Jonathan, after all your studies, you finally made it to the top-secret hideout where Darwinists keep all their overwhelming empirical evidence for evolution that they keep telling us IDiots about but never producing for us! :) bornagain77