32 Responses to “Let’s Recap: Darwin and Beyond”

1. 1.   Uncle Al Says:
   February 14th, 2009 at 12:26 pm

   http://www.mazepath.com/uncleal/evolve.gif

2. 2.   RBH Says:
   February 15th, 2009 at 11:12 pm

   Larry Moran will appreciate Carl’s emphasis on genetic drift.

3. 3.   tom Says:
   February 16th, 2009 at 9:59 am

   Can someone name me even a single controlled study or experiment on living, breathing animals (mammals, bugs, insects, fish, birds, etc) that proves darwin’s natural selection adapts populations genetically?

   You must prove natural selection, and you must prove the population changed genetically because of it.

   Anyone?

4. 4.   Carl Zimmer Says:
   February 16th, 2009 at 10:13 am

   Tom: For starters, you can read this: http://icb.oxfordjournals.org/cgi/content/full/45/3/456

5. 5.   tom Says:
   February 16th, 2009 at 11:02 am

   Carl…show me the mutations involved with the guppies and lizards. You have also not proven natural selection. Going to a site, observing a population, and then coming back to the site months or years later, only to see the population has changed is NOT scientific confirmation of how the population changed. The guppies may very well have changed epigenetically…and the lizards are probably just plasticity.

   show me the mutations, please.

6. 6.   Carl Zimmer Says:
   February 16th, 2009 at 11:13 am

   Tom: Scientists don’t have to find individual mutations to know that genetic changes have taken place. They can use other lines of evidence, such as showing that a trait is heritable. So, for example, the variation in the size of beaks of Darwin’s finches is partly heritable, as shown by the fact that parents with big beaks tend to produce chicks with big beaks. This kind of analysis can rule out other possible explanations such as plasticity, leaving selection as the only explanation that accounts for the evidence. This kind of approach has been well-established for decades, and you can find more information about it in a population genetics textbook.

   Biologists would love to see precisely which alleles are favored during natural selection and what new mutations arise along the way. But finding these is very difficult, like finding a needle in a haystack. (You have to be able to distinguish between changes that are neutral from those that are adaptive.) But that’s starting to change. See, for example, here: http://jb.asm.org/cgi/content/full/190/14/5087?view=long&pmid=18487343

7. 7.   tom Says:
   February 16th, 2009 at 11:38 am

   Carl…….epigenetic traits are heritable…surely you know that…..

   ..but so are plastic traits

   http://www.pitt.edu/~biohome/Dept/pdf/1632.pdf

   ….and so are traits derived from horizontal gene transfer….and probably many other mechanisms. If you care to call this stuff “science” then it is up to you (or the researcher) to PROVE it scientifically. IF one is going to claim evolution — and call it “science” — then he or she must do 2 things:

   1) he must prove that natural selection (as opposed to internal mechanisms) adpated the population.

   2) he must show that natural selection adapted the population genetically. If the trait arose as an epigenetic response to the environment, then this is not evolution. If a gene was laterally transferred via virus or taken up through a root system of a plant through the soil, then it is not evolution.

   Carl…you cannot keep claiming evolution without backing it up. You cannot keep patting darwinism on the back without proving it. You said this in your statement:

   “But finding these is very difficult, like finding a needle in a haystack.”

   Fine…I understand the difficulty. but the fact is, if you can’t find it — it may in fact not be there. But either way, if you can’t find it, then it’s not science….it’s more along the lines of wishful thinking.

   p.s…you really should know that ‘evolution’ does not equate merely to heritable traits. Adaptive “evolution” has a much more specific definition than that. It requires random mutation and natural selection…without both, there is no evolution.

   By the way — there’s no genetic variation in darwin’s finch beaks either.

8. 8.   Carl Zimmer Says:
   February 16th, 2009 at 12:27 pm

   Tom: You claim there is no genetic variation in Darwin’s finch beaks. What is your evidence for this claim? How do you explain the heritability of beak size, and the phenotypic variation in that beak size, if not through genetic variation? Before you set the standard of proof for biologists to meet, you’re going to have to explain such puzzling statements.

   Your objections also have logical flaws. For example, you claim that scientists must eliminate horizontal gene transfer before concluding natural selection has occurred. Horizontal gene transfer is simply another source of genetic variation in a population, like vertically inherited genetic variation. Also, in the bacteria experiment I pointed you to, the researchers used microbes that are unable to acquire genes through horizontal transfer, thus eliminating that possibility. Did you read that paper before responding to my previous comment?

9. 9.   Charles Schmidt Says:
   February 16th, 2009 at 1:20 pm

   Tom: It is easy to throw water on some else’s fire but that will not make yours brighter. Since you can find so much fault with what Carl said you must have your own answer to put forth. So what is your answer that can be backed you and tested? Just saying something is wrong does not make it so you must prove why it is and prove what you know is right.

10. 10.   tom Says:
    February 16th, 2009 at 2:18 pm

    Carl….the finches are not experiencing any change in their genetic sequence…the only thing that’s happening is that their bmp4 protein is being tweaked during development. This is an internal adaptive response to the environment. You cannot have evolution without genetic change.

    Notice how finch moms are also able to influence the birth (sex) order of their offspring when mites are around; boys first then girls:

    http://news.nationalgeographic.com/news/2002/01/0110_020110TVfinches.html

    “It turns out that finches are able to influence the size of their offspring by controlling the sex of their eggs according to the hatching order.”

    They’re also alble to speed up development in males. In this next link finch moms are able to inject extra hormones into offspring that come from “unfit” males:

    http://abcnews.go.com/Technology/DyeHard/Story?id=2494590&page=1

    “New research shows that a female house finch who gets stuck with a dull male can make up for some of his shortcomings by embedding an extra dose of hormones and antioxidants in the yolks of her eggs.

    It’s one of those miracles of nature that we never knew was there until a few years ago when scientists found that a female can deposit different amounts of nutrients in her eggs to give her offspring a better chance at survival.”

    And notice what they call it: a miracle.

    It’s no different with the finch beaks — there is no evolution: there is no genetic change…there is no natural selection — just a miracle. I know you scientists hate miracles, but that’s the way nature is; an unexplainable miracle.

    And Carl — horizontal gene transfer is not “just another source of genetic variation.” HGT bypasses selection and is generated as a purposeful response in individuals to environmental challenges. This process happens not by chance, but as an adpative response. This does not qualify as “just another source of variation” because the process is in itself sufficiently adaptive, without needing help from NS. NS is supposed to select from a pool of RANDOM genetic changes….but HGT is not random, which is why HGT was considered controversial, and even denied fiercely by evolutionists for decades.

11. 11.   Bryan Says:
    February 16th, 2009 at 2:54 pm

    Carl…”We are the supreme social species on earth”….????

    I think E. O. Wilson may beg to differ when considering ants.

    Your linkage between social prowess and intelligence may be dubious when considering them as well. They do just fine with relatively few neurons.

12. 12.   Mel Says:
    February 16th, 2009 at 4:10 pm

    When he refers to bmp4 in Darwin’s Finches, I presume tom is referring to work covered in this paper:
    http://www.sciencemag.org/cgi/content/abstract/305/5689/1462
    The finding was that there was heritable variation in timing and expression of bmp4 during embryological development of the finches. In other words, the differences in beak depth are due to bmp4 expression, but that expression, and thereby beak depth are controlled by other genes that can be altered by mutations. Tom, do you ever check your sources? You seem to repeat this same claim everytime you post, and yet have never looked to see if your interpretation is correct.

13. 13.   Carl Zimmer Says:
    February 16th, 2009 at 4:15 pm

    Tom: Sorry, but “miracle” was being used as a metaphor in that article. If you are going to deploy miracles as explanation, there’s not much point in arguing. I’m sticking with science here.

    And science shows, among other things, that horizontal gene transfer is not some precise process by which any microbe in trouble gets exactly the genes it needs. Lots of genes are moving between microbes all the time, and most of them are of little or no benefit to their new hosts. And if you’re going to claim that HGT was denied fiercely by “evolutionists” for decades, I’d love to know where you got that from. It was evolutionary biologists who established the widespread importance of horizontal gene transfer in the first place.

14. 14.   tom Says:
    February 16th, 2009 at 6:12 pm

    Carl…..I’m sure there are genes that are passed horizontally that are not adaptive. But those are not what I’m talking about. If genes get passed via virus that only infect the organism, then this would not lead to evolution, it would lead to death or sickness….so there’s really no point in discussing it. What I am interested in is adaptive traits…and in that case, specific genes can passed in response to need.

    http://www.sciencedaily.com/releases/2001/02/010220072315.htm

    “Scientists have long believed that bacteria in the intestines, known as Bacteroides, could exchange genetic information. Under certain conditions bacteria might copy and pass SPECIFIC (my emphasis) genes on to other bacteria which incorporate them into their genetic makeup, a process known as conjugation or horizontal gene transfer.”

    here’s an explanation why HGT cannot be considered “evolution”:

    http://www.eurekalert.org/pub_releases/2007-03/uoc–gag030807.php

    “Horizontal gene transfer is an alternative to Darwinian inheritance

    Relationship is not just by descent (in a vertical direction) but also horizontally among species that have no common ancestry but just happen to be in the same place at the same time.”

    and:

    http://www.trueorigin.org/bacteria01.asp

    “Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” However, analysis of the genetic events causing this resistance reveals that they are not consistent with the genetic events necessary for evolution (defined as common “descent with modification”). Rather, resistance resulting from horizontal gene transfer merely provides a mechanism for transferring pre-existing resistance genes. Horizontal transfer does not provide a mechanism for the origin of those genes.”

    HGT presents a problem for ToE because it is a nonrandom, purposeful, adaptive response by a fluid, dynamic genome. It turns out that all cells and organisms have the physiological capability to develop resistance, as opposed to being lucky enough to squeak through the selection process.

    I believe DNA in itself is not responsible for dictating traits because DNA is under strict control of the organism. DNA does not dictate life; life dictates DNA. The organism itself is a highly dynamic, adaptive entity…it uses and manipulates its DNA as needed. It can mutate its base sequence — or, different stretches of DNA can be inserted, deleted or amplified…..specific genes can be rerranged or recombined or mutated….genes can jump horizontally from one part of the genome to another, or from one organism to another…etc. Thus, the genome is in a constant state of flux….it is changeable at any moment. But none of these processes are random or accidental, but instead are under control of the cell, which is under control of the body as a whole.

    HGT is just one of these mechanisms of adaptive genomes….which is why it was ignored for decades by evolutionists:

    http://www.sciencedaily.com/releases/2005/11/051111103519.htm

    “The idea of lateral genetic transfer has been around for a few years, but what was missing was a good, hard, rigorous look at it,” Professor Ragan said.”

15. 15.   tom Says:
    February 17th, 2009 at 3:29 pm

    Carl? Where’d you go?

    Ok…so here’s how I see where we stand:

    I asked you for controlled study or experiment on living, breathing animals that proves darwin’s natural selection adapts populations genetically….to that challenge I received no controlled experiment, no verified mutation, no verified natural selection. Next you insinuate that I am being unreasonable for asking for this because pinning down evolution is like “finding a needle in a haystack.”

    Ok….so scientific evidence for evolution.

    Next…I claim finches do not experience a genetic change, of which you seem unaware of until I informed you about the bmp4 protein that gets re-expressed. Here’s a link if you need one — notice, no mutation mentioned. So down goes darwin’s finches as an example of “evolution,” as there is no change in the sequence of DNA.

    Next you claim horizontal gene transfer is just another “source of variation.”….to which I inform you that this cannot be true because darwinian evolution is a two-step process; chance variation paired with natural selection. But horizontal gene transfer, when it comes to adaptive traits, can hardly be considered random….especially considering specific genes can be transferred laterally upon need, as indicated in that link I gave you.

    Next, you tell me that the fact that mother birds can manipulate the birth order of their offspring, along with speeding up the development of their males, along with adding extra hormones to eggs that were sired by an “unfit” father is not a miracle….yet you don’t tell me how it happens either…..at the very least its unscientific and unexplainable — unless, of course you have an explanation.

    But anyway…I appreciate your input. I will be passing this discussion along to the members of Carm, of which I’m sure will come over and have a few things to say negatively about me. Hopefully it will increase your readership here at this blog, and maybe even help you sell some more books about evolution — which you have no examples of because it never happened.

    Cheers, tom

16. 16.   tom Says:
    February 17th, 2009 at 3:37 pm

    oh, here was that link:

    http://www.washingtonpost.com/ac2/wp-dyn/A64596-2004Sep5?language=printer

    “Darwin’s Finches, Continued

    Every high school biology student has heard the tale of Darwin’s finches. During his 1835 trip to the Galapagos Islands, Charles Darwin became obsessed with the immense variety of beak shapes adorning the islands’ distinct populations of finches — each one perfectly adapted to the kind of food consumed by that kind of finch.

    Those adaptations became Darwin’s prime example of how evolution worked and how, over time, natural selection could generate the world’s great diversity of species. But he never had a clue about how, on the genetic and hormonal levels, those beaks actually grew into their respective shapes during fetal development.

    Now scientists have finally cracked that egg.

    Clifford J. Tabin and colleagues at Harvard Medical School examined the role of a gene called BMP4, versions of which have been found in many animal species. The gene allows cells to make a hormone called bone morphogenetic factor 4.

    Scientists already knew that the hormone plays an important role in the development of bones. Tabin’s group went further by using sophisticated imaging techniques to see precisely when and where BMP4 and nine other hormones were produced in the beaks of fetal finches developing inside their eggs. Of the 10, only BMP4 activity correlated with final beak shape, indicating that the shape depends on when that gene is turned on in beak cells.

    In related work, Cheng-Ming Chuong and colleagues at the University of Southern California showed that BMP4 also accounts for the key structural differences between chicken and duck beaks. As final proof of BMP4′s key role, they altered those concentrations during development, giving rise to birds with novel beak shapes.”

17. 17.   Mel Says:
    February 17th, 2009 at 4:22 pm

    I think tom has definitively shown why he should be paid no mind whatsoever. Of course, his diatribe a while back about a world wide conspiracy between biologists and the media to hide “the truth” about evolution was also rather indicative of that fact.
    I continue to be amazed, though, that he keeps trumpeting the BMP4 findings without realizing that the gene to make BMP4 is under the control of other genes. Heritable changes in the expression of BMP4, as have been found in Darwin’s Finches, are in those controlling genes. That is very clear from the papers on the subject. If tom were at all honest, he would have checked to see if his interpretation was correct before using it as an argument. I also like how he just decided to ignore the links Carl directed him to. Oh well. He will make these same shoddy arguments again in a couple of months, and then again a couple of months later, and on and on and on.

18. 18.   tom Says:
    February 17th, 2009 at 5:12 pm

    Mel, regarding the BMP4, the point is that there is no mutation…no genetic change…no alteration in the sequence of dna…..what about this do you not understand? Do you not understand that it takes a genetic change to be considered “evolution?” How could you not know this?

    And yes, I did read the links Carl supplied….if you can show me the mutations or the controlled experiements verifying natural selection was the cause of change, please do so….

19. 19.   Norman De Plume Says:
    February 17th, 2009 at 6:02 pm

    I should point out that tom (aka Supersport, aka Guzman) is trumpeting his victory in out debating an “evilutionist” on a message board here:

    http://www.christiandiscussionforums.org/v/showthread.php?t=157348

20. 20.   Mel Says:
    February 17th, 2009 at 6:13 pm

    There is no mutation in BMP4, but in the genes controlling BMP4 expression.

    As for experiments verifying natural selection, the following list is from just two experimental systems. There are a great many more if you bother looking. You will notice that in a number of the papers listed, not only have the underlying beneficial mutations been identified, but their contribution to fitness increases have in fact been experimentally tested. I fully expect you to either ignore them, but I figure why not try giving you one more chance to prove you have some honor and intellectual honesty? If you do what you always do, you simply further erode your already non-existent credibility.

    Ostrowski, E. A., R. J. Woods, and R. E. Lenski. 2008. The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proceedings of the Royal Society, London B 275:277-284.

    Woods, R., D. Schneider, C. L. Winkworth, M. A. Riley, and R. E. Lenski. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences, USA 103:9107-9112.

    Ostrowski, E. A., D. E. Rozen, and R. E. Lenski. 2005. Pleiotropic effects of beneficial mutations in Escherichia coli. Evolution 59:2343-2352.

    Lenski, R. E. 2004. Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Plant Breeding Reviews 24:225-265.

    Sleight, S. C., C. Orlic, D. Schneider, and R. E. Lenski. 2008. Genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing and growth. Genetics 180:431-443.
    (abstract to the above: http://www.genetics.org/cgi/content/abstract/180/1/431)

21. 21.   Mel Says:
    February 17th, 2009 at 6:14 pm

    All of those were for E. coli. The next set describe an adaptive radiation that occurs with Psudomonas fluorescens in unshaken flasks. The first paper describes the radiation. The rest of the papers go into describing the genetic basis of the diversification.

    Rainey, P. B. & Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature 394, 69-72.

    Bantinaki, E., Kassen, R., Knight, C. G., Robinson, Z. & Spiers, & Rainey, P. B. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176, 441-453.

    Malone, J. G., Williams, R., Christen, M., Jenal, U., Spiers, A. J. & Rainey, P. B. (2007). The structure-function relationship of WspR; a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153, 980-994.

    Knight, C. G., Zitzmann, N, Prabhakar, S, Antrobus, R, Dwek, R, Hebestreit, H., & Rainey, P. B. (2006). Unravelling adaptive evolution: how a single point mutation affects the protein co-regulation network. Nature Genetics 38, 1015-1022.

    Goymer, P., Kahn, S. G., Malone, J. G., Gehrig, S. M., Spiers, A. J. & Rainey, P. B. (2006). Adaptive divergence in experimental populations of Pseudomonas fluorecens. II. Role of the GGDEF regulator, WspR, in evolution and development of the wrinkly spreader phenotype. Genetics 173, 515-526.

22. 22.   NP Says:
    February 17th, 2009 at 6:54 pm

    Tom also posts on the interwebs as “supersport”. Google him, and you’ll understand why it’s pointless trying to get through to him.

    People have explained to him before that the expression of the BMP4 protein is altered due to mutations in regulatory sequences, yet he will refuse to acknowledge that.

    Carl, you asked if he has read the paper you linked to. My best guess is that he hasn’t, because if he did he would have come across cited papers such as this one:
    http://gemi.mpl.ird.fr/PDF/Chevillon.BiolJLinnSoc.1999.pdf

    In dealing with creationists, we have those who are undecided and on the fence, and those who have already made up their minds. Unfortunately, I think the latter category consists of the majority and I will have to let you decide which category supersport falls into. Ironically, I’ve already made up my mind on that.

23. 23.   tom Says:
    February 17th, 2009 at 8:35 pm

    NP: “People have explained to him before that the expression of the BMP4 protein is altered due to mutations in regulatory sequences, yet he will refuse to acknowledge that”

    show me these mutations that have resulted in changes in regulatory sequences that resulted in changes in beak shapes and sizes.

24. 24.   tom Says:
    February 17th, 2009 at 8:37 pm

    Mel…what makes you think adaptive radiation is the same as “evolution?” Don’t just give me the papers — that tells me nothing….show me the evidence. Present a new trait, show that it was a result of mutation/selection.

    Can you just do that one simple thing for me?

25. 25.   Mel Says:
    February 17th, 2009 at 8:53 pm

    Adaptive radiation is not evolution to you? Thank you. You have shown you have no clue what you are talking about. Have you even thought of maybe taking a class or reading a couple of books about evolution? You don’t even know the definitions of the words you are using.
    By the way, I like how you just simply refused to bother with the papers. You do know they are where scientific evidence is presented, right? If you had even a rudimentary grasp of evolutionary biology, you would see that your questions, at least using the accepted definitions of the words you use in those questions, have been answered.

26. 26.   Mel Says:
    February 18th, 2009 at 12:52 am

    NP, I did as you suggested and looked at our little friend’s past. Wow. Just wow. Tom appears to be on the same level as the infamously dense Ken DeMyer. You have to wonder, though, if he is really as stupid as he seems, or genuinely insane. I honestly can’t tell, though it seems clear that he lacks reading comprehension and honesty at a minimum. Thanks for the recommendation. I won’t waste time with him anymore.

27. 27.   tom Says:
    February 18th, 2009 at 1:04 am

    Mel…don’t hide behind terms……if you’ve got an example of adaptive radiation whereby selection adapts a population genetically, show me. Until then we can all just assume your theory has no evidence to back it up. The “adaptive radiations” that I’ve read about (cichlids, lizards, etc) actually have no genetic change involved. But you’re welcome to show me otherwise.

    So go ahead.

28. 28.   tom Says:
    February 18th, 2009 at 1:07 am

    Mel: “By the way, I like how you just simply refused to bother with the papers. You do know they are where scientific evidence is presented, right?”

    show me….highlight the sections of the paper that explain how selection adapted animal populations…I need to see the proof of mutation and see the proof of selection…I want to see the quotes..the actual words.

    Put your money where your mouth is.

29. 29.   Mel Says:
    February 18th, 2009 at 1:41 am

    I gave you references. I won’t do your work for you.

30. 30.   roy Says:
    February 18th, 2009 at 3:52 pm

    Speaking as a law student, I would say that the only way to PROVE someone guilty is to get their confession. Otherwise, you just accumulate evidence and eventually, its enough to conclude they can’t be not-guilty, so they’re found guilty. If we only had jails with confessed guilty people, there would be a lot more mayhem on the streets. I think this guy seems to want something akin to a mathematical proof, or an utterance that asserts absolute logical certainty. From what little I know, that’s not what scientists do. If we only took medicines which were absolutely proven effective, we’d, well, not have any medicines.

31. 31.   Norman De Plume Says:
    February 18th, 2009 at 5:01 pm

    And thus we see the supersport debate tactic in full flow:

    SS: Show me evidence.

    *Shows evidence*

    SS (after not reading links): That’s not evidence.

    I should point out that this person (Tom on this thread) thinks that your eyes shoot out light to be able to see, that coffee enemas cure cancer and that every organism has the ability to adapt to any environment that it finds itself in instananeously.

32. 32.   Jo Says:
    February 19th, 2009 at 10:55 am

    “Evilutionists”? Is that the term they use? That’s HILARIOUS!

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