The Loom

Chew On This

Our ancestors branched off from those of chimpanzees some six million years ago. Since then, our lineage became human–and distinctly unlike other apes. Figuring out how that difference evolved is one of the grand challenges of biology. Until now, scientists have gotten most of their clues by looking at the fossils of extinct hominids. These fragments of bones only preserve a little information, but it’s not a random smattering of data. It’s more like a scaffolding on which other clues can be fixed, so that a picture of how we became human can gradually emerge. That’s because the changes documented in the fossil record were ultimately created through the evolution of our genome.

The power of combining fossils and genes was demonstrated today in Nature. Scientists at the University of Pennsylvania reported their studies on a human gene that has mutated into uselessness. Such broken genes are nothing new; scientists have identified several hundred broken genes in the human genome dedicated to smell alone. What’s striking about this particular gene, known as MYH16, is how important it is in its functional form to our primate cousins. MYH16 is a muscle-building gene that only becomes active in the developing muscles of the jaw. Apes and monkeys all have massive jaw muscles, which pass from the jaw up under their cheekbones, fanning out across the top of their skull and anchoring to a keel-shaped ridge. We have no such ridge, and we have pretty puny chewing muscles compared to apes. And much of the difference between us and other primates in this respect comes down a fatal mutation that hit a single gene: MYH16.

To get a better picture of this crucial event in our evolution, the Penn team compared our version of the gene to those found in primates and other mammals. By tallying up the changes each version of the gene underwent, they were able to estimate when MYH16 shut down in our own lineage. Their estimate: 2.4 million years ago.

This was no ordinary time in our history. Hominids before that age still had big anchoring crests and large jaws. Younger species had smaller jaws and smooth tops on their skulls. And something else happened at the same time: their brains began getting significantly bigger. It’s possible that when MYH16 still worked in our ancestors, their chewing muscles acted like a clamp on the evolution of brain size. The architecture of the entire top of the head was so dominated by the muscles and their anchoring that expanding the brain was impossible.

As fascinating as this result is, it’s important to keep in mind that we’re just at the beginning of this fusion of genes and fossils. Today’s report is actually the first to link some important fossilized trait with the evolution of a human gene. A few other studies have revealed some other genes that were also important in human evolution, although they leave a subtler mark on the hominid line. The language gene FOXP2 appears to have undergone intense evolution perhaps 100,000 years ago. There are probably several thousand genes that have evolved significantly since we parted ways with our fellow apes, and so it’s easy to blow these early discoveries out of proportion. While MYH16 may well have played a crucial role in our evolution, it didn’t do it alone.

For one thing, a hominid with a weak jaw can’t grind up tough foods the ways its ancestors did; it needs new foods. The oldest tools, interestingly enough, date back to about the same time as the MYH16 mutation. Scientists suspect that hominids were using these simple stone axes to hack meat off of carcasses and dig up tubers. This new diet might have meant that a mutation to MYH16 wouldn’t have mattered much. The new diet may have been just as important as the missing jaw muscles to letting the hominid brain expand. For one thing, a big brain requires lots of energy. One way to make more energy available is to shrink the size of other organs, and it turns out that we humans have one particulary small organ: our intestines. Other primates use their long bowels to digest tough foods poor in nutrients; we can survive on our abbreviated bowels because we eat better grub. So here’s a prediction: scientists will eventually discover genes that control the development of intestines in humans. When they compare them to ape genes, they’ll discover that they underwent an evolutionary change around the same time that MYH16 shut down. Our brains did not evolve in a vacuum; they coevolved with the rest of our bodies in a complicated dance of tradeoffs and feedbacks.

(I don’t want to turn every post about evolution in an attack on creationism, but here’s a parting question. MYH16 is clearly essential to the well-being of other primates. We have a copy of MYH16, but it doesn’t work. Where is the intelligence of this design? If we don’t need the gene, why did the designer insert it into our genome?)

Comments

  1. #1 Steve
    March 25, 2004

    Living Code guy Richard Gayle also does a good job with evolution and such. It’s important to fight against people who let politics and religion determine their science. I’m a physics student who’s slowly moving over to bio-flavored things, partly because evolution is such a beautiful and incredible idea. Once you get it, it’s obviously correct. When people argue, usually poorly, against it, it stuns me.

  2. #2 Brian
    March 26, 2004

    Carl suggests that developing tool use led to a change in diet which meant that disabling the jaw muscle gene would have no ill effect, and later positive effect of facilitating brain growth.

    I think you don’t need the assumption of a change in diet. Instead, tool use could simply substitute for some of the mashing and grinding power of strong jaws. If this is the case, small intestine genes may not have changed at the same time.

    Carl hints at another relevant point, that you can make more energy available by shrinking other organs. Disabling the jaw muscle gene is adaptive in and of itself – the body is no longer wasting energy building and maintaining massive jaw muscles. The fact that later mutations build on this for a completely different reason (making the brain bigger) is just one of the happy accidents that constitute evolution.

  3. #3 Fluffernutter
    April 9, 2004

    Chimpanzees, eh?

    Hey, which race do you think is “more evolved” : blacks or whites?

    A lot of people joke that blacks are “monkees”… and yet it’s the WHITES who have hairy bodies, light skin and thin lips! Shave a monkey and you’ll have a pale, thin-lipped little fellow with a 5 o’clock shadow.

    Therefore, whites are much more like monkees than black people.

  4. #4 John
    April 15, 2004

    OK, I think what we have here is a couple of real fools just trying to be funny.

    Not funny.

    What I would like to discuss, if discussion is still open, is the idea of scientific evidence. One thing is certain in science and that one thing is the simple fact that the most mundane science is not very replicable, especially if meta-analysis is considered.

    Results of the “scientific method” are very mcuh theoretically-based FIRST, rather than as a resultant of specific findings. And researchers, such as those represented here, often take previous “findings” as “fact,” when these findings are, IN FACT, far from factual and certainly, the findings are subject to speculation.

    All one needs to do to realize this simple reality is to meta-analyze these “findings” versus those of “psi” research. Psi research is a field largely considered a “pseudo-science” and yet the evidence of “PSI” is often 100′s of times more “provable,” according to the “scientific method” than what is being considered here today (on this topic of evolution).

    But, in such a specified field, what else can a specialist do but scoff at such a suggestion? Yet, I would be at fault if I did not inform you that this was the case. Evidence does not lie. However, theories often do!

    Good luck to you all. I respect your research here, but I suggest you broaden your scope a bit and take a good look at your findings. I would suggest, above all else, to reassess your explorations and move from a theoretical basis to a factual basis. Above all else, I would recommend a highly replicable approach… or in this case… you’re out of luck.

  5. #5 Joe
    April 16, 2004

    John, I’m not sure I know what you’re talking about, for a few reasons. First, your English is poor, which makes it hard to interpret. Second, your statements regarding science are wrong. You state that “mundane science is not very replicable.” By mundane, I’ll assume that you mean the type of science that many researchers, including me, perform every day in the lab. First of all, the basic tools that researchers use are derived from science that was itself worked out through replication. Second, the science that we do, based on this foundation, is repeated over and over _precisely_ so that we can determine its replicability. Once repeated experiments have shown its replicability, the finding is then tested and extended by logically bringing to bear previously replicated findings on this new observation.
    I’m also not sure what you mean by meta-analysis. If you mean analysis of a particular finding in a broader context, then you are again wrong. The growth factor HGF causes phosphorylation of its receptor, c-met. This is a particular replicated finding. In a broader context, many growth factors cause phosphorylation of their receptors (EGF, IL-2, SF-1, etc.). Since phosphorylation of these receptors invokes new gene transcription in cells, this can be abstracted even more broadly: Information is transmitted to cells by these proteins, and information is produced in response. Remember, all these results have been replicated and are available for your perusal in the scientific literature. If a new protein is discovered with similarity to known growth factors, then a good assumption to make is that it can be used as information which will give rise to new information. This assumption is, in fact, borne out all the time.
    My meta-analysis of psi-research, run along the same lines, would be as follows: no psi-experiment has ever shown replicable results. The end. You, however, seem to believe that this is not the case. If this is so, then I would like to see the psi-research that you state is “100′s of times more ‘provable, ‘” the evidence that you say “does not lie.” Remember, I said “replicable results.” Many scientists have spent considerable time researching psi-experiments without peer-reviewed publication of replicable results.
    Finally, it seems that you have reversed theory and fact with regard to science. The replicated and replicable findings that we mundane researchers come up with every day are the facts that we use in constructing our theories. These experiments, facts, and theories are all subject to criticism and change – this is a built-in part of science. For instance, it may be that some presumed new growth factors have no effects on cells – the reasons why are equally scientifically illuminating (concentration gradients, fine-tuning of the response, viral integration into the host genome, etc.) If anyone needs to broaden his scope, it is you.

  6. #6 John
    April 18, 2004

    You should read Dean Radin’s “The Conscious Universe” and get back to me.

    It was poorly reviewed (or reviewed incorrectly) by I.J. Good of Nature, International Weekly Journal of Science… and Nature eventually published an acknowledgement of the error and then, finally, a correction.

    The original Nature Review:
    http://members.cruzio.com/~quanta/review.html

    The rest of the story here, beginning with Radin’s response to the article:
    http://www.tcm.phy.cam.ac.uk/~bdj10/psi/doubtsregood.html#radin

    … and the whole series of exchanges, including Nature’s printed correction:
    http://www.tcm.phy.cam.ac.uk/~bdj10/psi/doubtsregood.html#radin

  7. #7 John
    April 18, 2004

    that last link should be:
    http://www.tcm.phy.cam.ac.uk/~bdj10/psi/doubtsregood.html#admission

    I’m going to attempt to HTML-ize these links for ya:

    Nature’s erroneous review:
    here

    Dean’s letter to Nature:
    here

    Nature gives in:
    here

    Or, summed up, for you:
    “Update of Aug. 14, 1998: In its correspondence pages (Nature 394, 413 (30 July 1998)), the journal has now belatedly published Radin’s letter (with the omission, no doubt not surprising given the Journal’s record, of his closing remark ‘I hope this note motivates readers to study the evidence for themselves’). A comeback by Good, still conforming to Rossman’s strictures of ‘obsolescent critique’, is appended to Radin’s letter. This is more than six months after the author originally requested of the journal publication of a note concerning the error, and more then eight months subsequent to my own similar request. The charge of censorship on the journal’s part is hardly affected by this belated response, perhaps made only in response to widespread complaints.”

  8. #8 John
    April 22, 2004

    Hey Joe,

    I’m so glad you used the term “fine-tuning.” “Fine-tuning” is the greatest scientific term ever invented, isn’t it?

    If you get results that aren’t what you wanted in “real science,” you can chalk it up to a “dirty test tube.” This is what was alluded to when I spoke of “meta-analysis.” Let me explain…

    You will be quick to argue that the method of testing is an important consideration and that various methods can’t all be given the same importance, if certain methods themselves were faulty. Coincidentally, this is the point I was making with Psi research. However, taking into account all the supposedly “failed” psi research, it becomes evident through meta-analysis, that these findings support the existence of Psi much more than they discredit it.

    Certain people have claimed the mapping of the human genome was downright proof of evolution, for all those “bible thumpers” who doubted. What about all us “All Is Oners” dating back to 5,000 BC? What about Shrödigner who stated that, somehow, everything was all the same thing? Bohm and Quantum Theorists, Nonlocality, etc? The Vedanta?

    Really? The human genome “proves” evolution?

    Gene Myers, the computer scientist who actually put together the genome map, said this when questioned about the possible origin of the genetic code:

    “We don’t understand ourselves yet . . . there’s still a metaphysical, magical element. What really astounds me is the architecture of life. The system is extremely complex. It’s like it was designed.”

    And, well, does an apparently “designed” system require a “desiger?”

    Myers continues, “There’s a huge intelligence there. I don’t see that as being unscientific. Others may, but not me.”

    Finally, scientists are trying to decipher how the genome mechanism works, but they haven’t a clue about how the procedure originated, or why. In an article titled, “Messages from the Genome,” which appeared in the December, 2000 issue of Harper’s Magazine, Arthur Cody describes the operations within the genome as a series of “triggering” processes. One thing triggers another, which triggers another, etc. He then raises this question:

    “What triggers the triggerer? Nobody knows. More than that, nobody has any theoretical proposal to suggest . . . . ‘Triggering’ is an interesting biological event; it goes nowhere toward explaining construction. What kicks the homeotic gene into action? No answer exists, factual or theoretical . . . . Not only does no one know, no one has the slightest idea how to look for an answer . . . . Everything truly essential about the process is utterly and even radically incomprehensible.”

    The human genome is made up of the chemical compound, DNA. The building blocks of DNA are units called nucleotides, composed of a sugar, phosphate and a nitrogenous base. All the origin of life scenarios fail to explain how such nucleotides can form naturalistically in the manner that would then cause them to form a string of nucleotides.

    Then there’s the issue of the origin of DNA molecule itself. Sir John Maddox, former editor of the prestigious Nature magazine, in 1994 lamented, “So it is disappointing that the origin of the genetic code [DNA] is still as obscure as the origin of life itself.”

    One scientific reason why we didn’t evolve from lower life forms over the alleged “millions of years” is the genetic repair system found in the nucleus all living cells (and in prokaryotes that don’t have a nucleus). This complex system continuously monitors the DNA molecule for mispaired bases and damage and is a major roadblock in allowing genetic mistakes (mutations) to establish themselves in DNA. Unfortunately for the materialist, it is these random mistakes upon which the cryptic macroevolutionary process depends. If neo-Darwinian theory were true, then natural selection would clearly select against these efficient repair mechanisms.

    Our alleged bacterial ancestry is without scientific support. If such a bizarre progression occurred, it left no fossil evidence, “Both the origin of life and the origin of the major groups of animals remain unknown” said evolutionist A.G. Fisher in 1998. Editor of the American Scientist book, ‘Exploring Evolutionary Biology’, stated, “The fossil record has always been a problem.” A problem for macroevolutionists perhaps, but certainly not for the creation science model which predicts the abrupt appearance of life in the sedimentary rock units. Humans are a good example. According to evolutionists Villee, Solomon & Davis, “We appear suddenly in the fossil record, or so it seems to many paleontologists.” In 2000 two evolutionists, Collard and Wood admitted, “existing phylogenetic hypotheses about human evolution are unlikely to be reliable. Accordingly, new approaches are required to address the problem of hominin [evolution].” The same can be said for animals, “Despite a century of work on metazoan phylum-level phylogeny using anatomical and embryological data, it has not been possible to infer a well-supported [evolution of the animal kingdom]” Annual Review of Ecology & Systematics, 1994.

    Check out how frequently Brian Green uses the term “God” (and not in a cosmic time-clock kind of way) in his “Elegant Universe.” It is actually a surprisingly good read.

  9. #9 Joe
    April 22, 2004

    John-

    You mentioned Dean Radin’s name. I read the first chapter of his book, and it is clear that he misrepresents the history of psi-acceptance in arguing for his 4-stage model. The unquestioning historical acceptance of these notions is absolutely unlike the model he proposes. The notion that he is on the cutting edge of research that will bring in an age of psi-acceptance is convenient for his purposes, but that research is suspect. He claims that statistical analysis of his experiments show statistically significant deviations from randomness, but this claim has been called into question (http://www.skepticreport.com/psychics/radinbook.htm). A PubMed search revealed two papers in the not-well-respected Journal of Alternative Medicine, one of which dealt with the effect of prayer on astrocyte growth and found no effect over three days (but did claim to find, again, a slight, statistically significant deviation from randomness on one day of the experiment.) I don’t know enough statistics myself to analyze the data, but the above explication of his statistical misrepresentation fills me with a healthy disinclination to trust his statistics.

    Next, you misunderstood my use of “fine-tuning of the response,” assuming that I was alluding to some type of indefensible fudge factor, the “dirty test tubes” which you spoke of. Nothing of the sort. The growth factors and receptors I mentioned signal information in a linear fashion, not an either-or fashion. These mechanisms to decrease or increase the information flow are the fine-tuning I spoke of.

    With regard to meta-analysis, it seems that Radin wants to lump together a number of different experiments performed at different times by different labs and analyze them statistically. This is never scientifically performed because it doesn’t mean much. I myself have done experiments over months in which the absolute values of a particular phenomenon have varied drastically; these values cannot be meaningfully compared to, say, another lab’s. The general observation is the subject of meta-analysis, not the individual experiments.

    With respect to the Human Genome Project: Here, I agree with you. This no more proves evolution than any other scientific observation over the years. Rather, the sum total of these observations leaves no doubt. Evolution has been observed not only in the lab but in the wild. Finches in the Galapagos, cichlids in South America, stickleback in Canada – all these organisms show evolutionary responses to man-made as well as natural stimuli. The genome of all these organisms has been designed by evolutionary pressures, as has ours – no wonder these genomes are complex, mystical, magical, and metaphysical. There are many religious scientists; I’m sure the Human Genome Project was a source of inspiration to them on many levels.

    The Cody quote, ellipses and all, is describing the process of embryonic development with its description of homeobox genes, which are sets of genes that are necessary for specific developmental processes such as limb formation. As such, their triggering mechanisms are known – remember the growth factors I talked about earlier? And the fine-tuning of that response? Here is one instance where this fine-tuning comes into play. Seems like Cody is referring to something else with his question about construction – could he be a religious scientist, or one who has sympathy with some form of Intelligent Design?Is he even a scientist? Can’t tell – you’ve left out all pertinent information.

    With regard to your nucleotide section, their are quite a few theories that explain their natural synthesis and adaptation for use as information carriers. Perhaps you passed them over in your hurry to arrive at a conclusion. DNA repair is not a perfect mechanism, contrary to your implication, and, among other mechanisms, the built-in redundancy of the genetic code allows for necessary mutations to occur during times of evolutionary stress.

    Your assertions concerning the fossil record are absurd – luck is the only reason we have as many fossil organisms as we do. During this discourse, you have revealed yourself to be a creationist who believes that the Earth was created 5,000 years ago by an Intelligent Designer who gave us psi-powers. You ignore scientific arguments and denigrate the scientific method while using a method of communication that could not have been built without it. Evidence for psi-powers is unsupported; Intelligent Design has been debunked. I’ve responded to all of your points; you’ve responded to none of mine. I will not continue this discussion.

    Joe

  10. #10 John
    April 22, 2004

    In many cases, Creationists and Evolutionists are polar opposites set on disproving the other: “what the thinker thinks, the prover proves.” Were it not for each other, neither would have a specific viewpoint to assert. This is what’s good about life and why life is what it is. Arguments often dissolve with both sides convinced they have disproven the other.

    I actually wouldn’t consider myself to be a “Creationist,” simply because I see evidence for an as yet “officially” unrecognized force (or perhaps “unofficiall” recognized would be a better term?) which permeates the universe. Belief in “Cosmic Intelligence” (or an intelligent force underlying everything) is different from “Creationist” for many reasons, which at first might be hard to distinguish for someone who simply sees order as the natural result of chaos. For the sake of brevity, you could dismissively state, “order comes from chaos,” but if I asked you why, you’ll be stuck with one of a few answers: “because it just does” or you could show me a Mandelbrot set or launch a Cellular Automata program (which wouldn’t explain why; the would describe how), OR you could just say, “that’s what we’re trying to figure out, dumbass!” Finally, you could be totally dismissive and say, “The question “why” is illogical as it is attempting to find purpose in the universe, which necessitates a Godhead.”

    But, I’ll try anyway to explain why I’m not a “Creationist,” anyway… for starters, I don’t believe in any Gods I’ve read about here on planet Earth, nor do I believe in any Godhead which has created all of “creation.” I merely see that a “thing” only exists in relation to some other “thing” and that both “things” are actually the same “thing” underneath this illusion of separateness. We now realize that the universe is not made up of “separate things” at all, but a “whole thing” of “stuff,” which only appears to be “separate things” when looked at through the spotlight of narrow focus… until the point of extremely narrow focus when this illusion finally breaks down and we realize we don’t know what the hell this “stuff” really is at all. All respected men who have examined this stuff has said as much, with a tone of total awe and consistent surprise.

    Consciousness is a hard thing to pinpoint and the minutae of reality we examine to understand and apply this knowledge on a grander scale is exactly what we think it is: smaller “parts” of a whole. We grasp the universal reality in small bits, deciding “this thing” goes with “this thing” which goes with “this thing” which goes with “this thing”… In experiments, we are often careful to realize that our own consciousness, subconsciousness or unconsciousness might interfere with a true outcome, so we take every precaution to eliminate all possibilities in which we could inadvertantly taint the results. This is a logical, intelligent decision on our part. Yet, while logic is a result of labelling and ordering our world, logic “goes with” consciousness and consciousness “goes with” brain, which “goes with” neurons which “goes with” electrochemical reactions which “goes with” the total organism. Whatever consciousness actually is, all organisms have some degree of order within the environment of which they are part. Questioning “why” there is order is just as necessary to understanding the universe as it anything else because it is the very same thing that allows us to examine anything in the first place. If there was no order, there would be chaos, if if there was chaos, there would be no logic. Therefore, the question “why is there order?” is not illogical and it does not necessitate a Godhead. It is simply asking, “why the implicate order of all this ‘stuff’?”

    And you could still respond with, “That’s what we’re trying to figure out, dumbass!” But, trying to extrapolate your consciousness from an unconscious system seems just as insane as claiming that the universe is not really an ordered or logical system at all, but just a temporary result of chaos which will eventually return to chaos. But, you know what? That is Vedantic belief, which predated the Big Bang theory by thousands years.

    I would recommend the rest of Dean Radin’s book simply for entertainment purposes, if nothing else. I was ready to put it back on the shelf after that Preface, which struck me as supremely lame, but the rest of the book I found very interesting.

    In addition, Alan Watt’s “The Book” might better explain what little I said above.

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