Wednesday, April 24, 2013

Nothing in Biochemistry Makes Sense Except in the Light of Evolution

The title of this post is a slight paraphrasing of Theodosius Dobzhansky's famous saying, "Nothing in Biology Makes Sense Except in the Light of Evolution. That was the title of an article he published in American Biology Teacher and that's significant since the main point was to convince teachers that evolution is important.

What applies to biology also applies to biochemistry. Evolution should come up in many places in a typical biochemistry course. The most obvious place is when we teach comparisons of nucleotide and amino acids sequences and the construction of phylogenetic trees. Students have to know the underling concept behind these comparisons. The have to know why some sequences are conserved (negative selection) and why some sequences are variable (fixation of neutral alleles by random genetic drift).

But this isn't the only place where evolution is important. How can you explain why humans need vitamin C and "essential" amino acids without mentioning evolution? How can you teach biochemistry without covering the evolution of biochemical pathways? How do you explain the existence of a complex process like the membrane-bound photosynthesis complexes in chloroplasts without showing how it evolved from simple bacterial examples? Who teaches the information flow section of the course without starting with E. coli and working toward the more complex eukaryotic examples? How do you explain why animals need glucose when most species don't need an external supply of complex carbohydrate? How do you explain why gluconeogenesis is a more primitive pathway than glycolysis? Why are comparative genome studies important in working out metabolic networks? Why does "homology modeling" work?

The American Society for Biochemistry and Molecular Biology (ASBMB) is trying to set up a certification scheme for biochemistry programs in America. The idea is that universities and colleges that meet certain standards would receive a stamp of approval from ASBMB. There would be a nation-wide exam for graduating students and if they pass the exam they get a sort of "certification" that proves they have the minimum skills and knowledge to take jobs that require these skills.

The trick is to define the common skills and knowledge that are needed. I attended two sessions at EB2013 where these criteria were discussed. One was a presentation by the committee in charge followed by some discussion: "ASBMS Certification Program for Bachelor's Degrees in Biochemistry Molecular Biology and Related Majors." The questions in this session were focused on how to get certified and not on what was in the proposal.

The other session was "Promoting Concepts-Driven Teaching Strategies in BMB Through Concept Assessments" but, as it turned out, there was very little chance to discuss the concepts that were being assessed.

You can read the current draft proposal by clicking on the link at ASBMB Degree Certification Program in Biochemistry and Molecular Biology. You might be interested in finding out what a department needs to do in order to be certified.

I'm more interested in what biochemists have to teach. Here's the relevant section ...
Core Concepts and Learning Objectives

An ASBMB-recognized program should be able to relate each element of its BMB curriculum to one or more of the core concepts listed below and their related learning objectives (For reasons of space, sample learning objectives are provided in Appendices II – V):

1. Energy is Required by and Transformed in Biological Systems.
2. Macromolecular Structure Determines Function and Regulation
3. Information Storage and Flow Are Dynamic and Interactive.
4. Discovery Requires Objective Measurement, Quantitative Analysis, & Clear Communication.

The curriculum should present these core concepts in a manner that illustrates the pervasive role that Evolution plays in shaping the form and function of all biological molecules and organisms.
That last sentence is new to me. I've never seen it on any of the slides shown at either of the meetings I attended (EB2012 and EB2013).

It's a welcome addition. But, since most biochemistry courses in America are taught out of Chemistry Departments, I wonder if this will make certification more difficult.

Finally, I can't help but insert a plug for my book. It's the only biochemistry textbook that presents the subject from an evolutionary perspective and it's certainly the only textbook where the pervasive role of evolution is emphasized in every chapter.

The next step will be to help the organizing committee refine and upgrade the "Learning Objectives" for each of the core concepts. These are given in four appendices in the draft document.


Dobzhansky, T. (1973) Nothing in biology makes sense except in the light of evolution. American Biology Teacher 35:125-129.

49 comments :

  1. "The have to know why some sequences are conserved (negative selection) and why some sequences are variable (fixation of neutral alleles by random genetic drift)."

    And, of course, they should know why variation in many biochemical traits in a comparative context reflects directional selection to local environmental variation.
    (reference)

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  2. Really? What evolution? Because being on this blog for few months I have learned that there are at least 3 three evolution theories... Boy... I hate to be a shit disturber but lets look at what evolution type makes sens to this guy and Larry.

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  3. I mean biochemical evolu-shit makes no sense. Neither does the macro? Which one does? Micro-evolution? Well, possibly..

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    Replies
    1. That you are too ignorant to know why and how it makes sense is very different to something not making sense. get an education. I have told you before. You truly have no idea how stupidly ignorant you sound. Imagine that I went to a Christian blog and started saying how it does not make sense that Mohamed was married to Joseph and Huehueteotl before they decided to sacrifice Mary and how Jesus was born from Mary's ashes and then killed his father. Yes, that's the level of stupid and nonsense that you display. Not knowing anything you come with this attitude (as if you knew anything), and start talking nonsense to people who do understand the stuff you are criticizing with your background of utter ignorance.

      I can't stress it enough: get an education. At least when you come strive to understand and don't comment until you have grasped the stuff properly. I can recommend a few basic educational web sites, maybe some very basic books to start, if you are willing. (Who am I kidding? You? Interested in learning? Nah, you only care to come and display your pitiful ignorance.) If you want to reject evolution in ignorance, fine, but then don't come commenting on things you don't really understand. If you want to comment how wrong these things are, then make sure that you understand what you are criticizing. It's that simple. It requires a lot of self respect. Do you have it? I doubt it, but we will see. I bet we will see soon, and that you will only confirm my diagnoses.

      Delete
    2. @Negative

      I have been educating myself and look what I found at the first try:

      DNA has the following:

      1. Functional Information
      2. Encoder
      3. Error correction
      [4]. Decoder

      Can you please show me in a step by step fashion how such a system could randomly without any intelligence, and totally unguided build itself?

      Where did the functional information come from? What was first? The encoder? The decoder? Error correction? Functional information?

      This is an irreducibly complex system and when any part is removed the system fails to function. Can you prove otherwise?

      Delete
    3. @ Dominic

      First you need a grounding in population genetics. Read this, and get back to us.

      http://evolution.gs.washington.edu/pgbook/pgbook.pdf

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    4. Dominic,

      Being indoctrinated in IDiot parlance is not the same as educating yourself. What you wrote shows that you have some cartoonish idea about evolution and science. This is why I told you to get an education. For example, despite being told several times that evolution is not pure randomness, you keep talking about it as if it was mere randomness. Your list of affirmations seems rather odd and off:

      1. What the hell is functional information? How do you measure it and compare it?
      2. What do you mean when you say that DNA has an encoder? I could not match this to anything I know about DNA.
      3. DNA has no error correction. The process of copying it does. Is this what you meant?
      4. DNA has no decoders, maybe you meant the mechanism of translation or the whole thing from DNA to RNA to protein (when proteins are produced, because lots of genes don't code),

      Can you please show me in a step by step fashion how such a system could randomly without any intelligence, and totally unguided build itself?

      Here you make the mistake of equating evolution to mere randomness. With such a huge mistake, I would not know where to start explaining how things like this could have evolved.

      Where did the functional information come from? What was first? The encoder? The decoder? Error correction? Functional information?

      To understand this you would have to first define functional information, and understand how processes involving random variation plus selection can solve very complicated problems. Go study a lot about information proper, and about genetic algorithms, then read a bit about directed evolution, and about the theories about an RNA world. That might give you a few clues. But read from places that want to educate you, not in creationist sites (such as ID sites), because the creationist don't want to educate you. They want to indoctrinate you. Remember, I am not asking you to believe any of it, but to properly understand it. Properly! I insist, properly!

      This is an irreducibly complex system and when any part is removed the system fails to function. Can you prove otherwise?

      This shows not only that you don't understand evolution, but also that you don't understand how science works. Anyway, I don't need to prove otherwise. We have had mutants that lack error correction, for example, and they survive. A little sick because they easily get mutations, and some of these mutations kill some cells. I worked with some such cells. They were supposed also to be unable to produce a particular amino-acid. Yet, because they had no repair, they would readily mutate back to producing the amino-acid ...

      But I'll save you time looking for one that will make me stumble. I can tell you that we don't know the evolutionary history of each and every system, and that there must be some systems that cannot be reduced as they stand today. That does not mean that those systems could not have evolved. You still need to understand what you are talking about before continuing to argue. Your comments have mistakes that betray your lack of a proper education. If you don't know what you are talking about, what makes you think that you have any convincing argument against evolution? You have no idea, therefore you are the authority? I insist, if I made malformed questions and affirmations to challenge Christianity, mixing and matching misunderstood and half heard stories from all kinds of mythologies, and then I put some nonsense on top, would you take my challenges to Christianity seriously?

      Get an education! Stop already displaying such ignorance and get proper understanding before commenting. Otherwise just shrug in your ignorance and stop displaying it.

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    5. @Dominic
      I have been educating myself and look what I found at the first try:

      DNA has the following:

      1. Functional Information

      Haha, if that's what you found then you haven't been educating yourself, you've been reading creationist propaganda.

      DNA has information in certain specific contexts. One piece of DNA might contain the information about how to build a specific protein, but that information might not work in all organisms, because they live in different environments. You can be pretty sure, for example, that most of the enzymes that work inside your cells, would be functionally dead inside a bacteria that lives at 90 degrees C in a hydrothermal vent. So the "functional information" in DNA is contextually specific, it is not an intrinsic property of the string of DNA itself.

      In any case, it got mostly there by natural selection. Selection takes environmental information and slowly builds it into DNA sequence. Temperature adapatation is a classic example of how environmental properties can yield selective pressures that change the sequence and function of DNA and therfore ultimately, enzymes and structural proteins of all kinds. This proves that natural selection is the source of "functional information".

      Google scholar "temperature adaptation" for bacteria, maybe include "experimental evolution". Get educated.

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    6. 2. Encoder

      What? DNA doesn't have an "encoder". Mindless gibberish. This is where that basic molecular biology education you never had would do you well.


      3. Error correction

      Not always, and not in all circumstances. In fact, some processes important for your survival actively rely on high error rates, e.g. mutations. One is somatic hypermutation in evolving immune system antibodies (immunoglobulins).

      Viruses like the Flu and common cold are RNA viruses that invade our cells and take control of gene expression(in order to make new viruses). They intentionally shut off DNA error correction in order to get high mutation rates when they develop new coating proteins(which they rely on in order to invade cells and avoid the immune system). This allows them to adapt to our immune systems (which is why in return, our immune system has evolved to shut off it's own error correction and increase the mutation rate up to a millionfold in order to "keep up").

      If the flu and common cold did not shut off our error-correction machinery, our immune-system would out-compete them and flu and common cold would probably go extinct world-wide in a single year.

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    7. [4]. Decoder
      More gibberish. Maybe if you had even a cursory understanding of the subject you'd be able to articulate, using proper terminology, what a DNA "decoder" is.

      Delete
    8. @Rumraket, Negative Entropy, TheOtherJim

      Here is more details regarding the issue. Feel free to educate yourselves and then comment here or join the discussion on UD.

      http://www.uncommondescent.com/irreducible-complexity/andre-asks-an-excellent-question-regarding-dna-as-a-part-of-an-in-cell-irreducibly-complex-communication-system/

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    9. Dominic,

      You can't read can you? What did you not understand of my answer?

      Have you asked yourself why kairosfocus did not show the biological processes, but rather those engineering diagrams? I will tell you one reason: your points make no sense, so he had to concentrate in trying to make the whole thing look designed. Kairos is an openly dishonest self-deluded, self-rigtheous ass-hole, and I will not engage in talking to him about anything.

      And I told you, there is nothing irreducibly complex about what you wrote. That if I am charitable enough to translate each point into something that does make sense (the one that's unmatchable is that part about encoders), because as they stand they are nonsensical.

      This is why you ran there. Right Dominic? Instead of educating yourself you get to have the nastiest pieces of shit in creationism to support you. Not only are you ignorant, you are willingly so, and then you're a coward. You won't learn yourself, you have to call your big brother kairos to fight for you, to defend your nonsense. You know that he can fling bullshit with great effect, and so he did. Enjoy your UD echo chamber of craziness. My brain hurt as soon as I read the entry and a few of the comments. What a bunch of self-reinfocing imbeciles.

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    10. Oh I see. Dominic, you just copied someone else's bullshit. This is why you have no idea what my answers might mean. You have no idea what that "Andre" at UD pretended these points to be. What a joke of a human being you are. You copy someone else's comment expecting to pass for being educated, then you pretend that some bunch of ignorant and stupid creationists at UD congratulating each other on their misunderstandings of evolution counts as an answer and as education.

      If that's how you are educating yourself you will not get very far. You only confirm your need to truly get an education. Now either do so or just shut up.

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    11. LOOOL, Dominic simply copy-pasted questions another guy asked of Matzke and utterly fails to understand the answers he's been given. Fuck, HE DOESN'T EVEN UNDERSTAND THE QUESTIONS HE COPIED.

      What an utter, utter fucking joke.

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    12. I noticed nobody joined the discussion on UD. I didn't expect that. Here is pretty much the same. You tell me to get educated, I go and do it, and now you have no arguments, so you resort to name calling and swearing. Hmmm... Speechless scientists lol

      Delete
    13. You didn't go and got educated Dominic, I warned you against indoctrination in creationist places, but you did worse than go get indoctrinated at creationist web sites, you went and copied somebody else's questions, not caring to understand one bit. Not one bit about the questions, not one bit about our answers (we gave you answers Dominic, check above). You are a sad excuse of a human being. If that's the way you want people to think about believers, you did a great job. It's people like you who have convinced me of the merits of militant atheism. Creationism tends to destroy both the intellect and the most basic honesty of a human being. Remember this next time you come and post something: your ignorance and dishonesty work against you and against your beliefs.

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    14. You tell me to get educated, I go and do it....

      No, you did not do it.

      The first step in getting an education applies to exercising discrimination about what you're setting out to learn. If I told you to get an education in archaeology and your came back spouting garbage about ancient astronauts from Nibiru, Atlantis, and repeated planetary flybys as the reason for the miracles recorded in the Old Testament, then you would not be one iota more educated about archaeology now than when you began, even if you had read dozens of books and articles.

      Delete
    15. dominic said:

      "I noticed nobody joined the discussion on UD."

      If what you're saying is that no evolutionists joined the so-called discussion it's because UD blocks and bans the vast majority of comments from evolutionists. The only reason they ever allow any comments from an evolutionist is because they want to fool people into believing that they're open to honest discussion, and because they need someone to sanctimoniously preach at, and because UD would otherwise be DEAD.

      Essentially, UD is DEAD, and has been for a long time. The IDiots who still post there just won't accept reality, in all kinds of ways.

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    16. I would like to assemble a cell by accident. What should I do? I wanna put everything in the test tube and then assemble by accident the cell in perfect conditions. Please tell me what I should do to make evolutionary theory believable because my 8 year old son told me to get a life. Any ideas?n

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    17. @The whole truth

      Why don't you join the blog at UD. Just prove them wrong. You have my support. I don't like creationists that much so, if you prove them wrong, I will not lose my sleep. Love Dom

      Delete
    18. I would like to assemble a cell by accident. What should I do?

      You can't assemble a cell by accident. Cells were not "assembled". But wait a minute, there is a way! You can prove creationism right. Pray to God to create a cell for you -- or maybe even some bigger critter, a whale or something, like he did in Genesis.

      Delete
    19. dominic said:

      "Why don't you join the blog at UD. Just prove them wrong. You have my support. I don't like creationists that much so, if you prove them wrong, I will not lose my sleep. Love Dom"

      Obviously you didn't read what I said. I did sign up at UD, before I ever said anything against ID on any website and before I ever used The whole truth user name. I was civil and just asked a few relevant questions. My questions were put into moderation, so I waited a few days and asked again, and I was then banned.

      A year or so later I tried again with another user name and the same thing happened. Moderation and then banned. Many other people have had the same thing happen to them.

      UD is a den for dictatorial, two-faced, lying, sanctimonious, arrogant, goose stepping, ignorant, scientifically illiterate, shit spewing, insane bible thumpers with delusions of godhood.

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    20. Piotr Gasiorowski:

      "You can't assemble a cell by accident. Cells were not "assembled". But wait a minute, there is a way! You can prove creationism right. Pray to God to create a cell for you -- or maybe even some bigger critter, a whale or something, like he did in Genesis."

      How do you think the first "simple cell" came into existence? If it was not created, then at one point one of the components had to "learn" how do build a cell membrane.
      You believe it was done by hocus pocus abracadabra?

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    21. Milosh,

      You believe it was done by hocus pocus abracadabra?

      Nope, it is creationists who think it happened that way.

      then at one point one of the components had to "learn" how do build a cell membrane

      Learn? Amphipatic molecules form membranes and other curious structures quite by themselves without having to learn anything.

      Delete
  4. I hope you don't mind being remembered in the future as Professor Moron!

    (Publish that if you have balls!)


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    Replies
    1. Yes, because your comment is so hard-hitting and all....

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    2. "I hope you don't mind being remembered in the future as Professor Moron!

      (Publish that if you have balls!)"


      Is that what they teach children these days at Sunday Mass?

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    3. @Pedro Pereira

      Based on my recollections, yes, this is pretty much the substance of the message promulgated by the RCC.

      And speaking of balls Pépé, based on the evidence, those seem to be vital items for a catholic priest, and apparently they are not just there for decoration.

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    4. Someone whose name is "Pépé" should not be swapping out the vowels in other people's names. Would you like us to do that to you, Pépé?


      Delete
  5. Oh!

    You do have balls!

    Vital items for a Darwinian...

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  6. Larry, a more important point than even the ones you have made is that many of the students in Biochemistry classes are headed to medical school. They need to know that biochemical systems are closely similar in other mammals to what we find in humans. People assume this when they study model organisms and use the biochemical knowledge to shed light on human biochemistry. They forget that this is the result of common ancestry, that they are assuming that related organisms have similar biochemistry,

    Creationists who are MDs often declare that they don't use evolution either in the practice of their medicine, or in teaching it. But they are forgetting the "elephant in the room", common descent, whenever they make use of insight from model systems.

    Without that, we would have no reason to believe that the biochemistry of a macacque was any more similar to ours than the biochemistry of a mushroom.

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    1. This is not accurate.
      First one just needs accept the sameness of a macacque to me without any interest in ideas of origins of either./ Its just a raw fact unrelated to anything else.

      In fact also creationism teaches and always did that nature was created from the same creator AND so biology , as in physics, would easily and most likely be based on the same principals.
      All nature has eyes, ears, and feet, and stomach etc and for the same reason.
      The god of physics is the god of physics of biology.
      In fact its evolution that should be teaching great diversity in biology due to the glory of mutations creating everything to be selected on.
      Common descent actually hides a lack of diversity in biology as should be really the result if evolution had ever been true.
      MD creationists do fine and probably better then anyone else.

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    2. All nature has eyes, ears, and feet, and stomach etc and for the same reason.

      I know being a creationist requires massive amounts of ignorance of the living world, but still... do you ever step away from the computer and outside your house? Do you realize that plants, fungi, algae, bacteria, etc. are part of nature and not just God's set design? Do you realize that there are more animals than just tetrapods in the world? Have you ever seen an earthworm? A jellyfish? A sponge?

      Common descent actually hides a lack of diversity in biology as should be really the result if evolution had ever been true.

      Well, that answers that question: you really must be a permanent shut-in.

      MD creationists do fine and probably better then anyone else.

      Tell that to Baby Fae.

      If you're representative of what we might expect if creationism takes over, then one can only conclude that we'd be losing everything we've learned about biology since Aristotle.

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    3. "First one just needs accept the sameness of a macacque to me without any interest in ideas of origins of either./ Its just a raw fact unrelated to anything else"

      In other words, stay willfully ignorant. I yield to you as the expert on that Nyers.

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  7. I should have written, more clearly " ... was any more similar o ours than was the biochemistry of a mushroom".

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  8. Mr Moran.
    I know someone this year getting top top marks in biochemestry class in a university.
    There is no need to understand or include evolution into the subject.
    Biochemistry has nothing to do with evolution but is in fact a very practical realtime breakdown of nature.
    Its just a added speculation HOW the present results of biochem CAME about.
    In either case kids are just memorizing what they read and inclusion or exclusion of evolutionary ideas in biochem is unrelated to a final score or understanding of realtime biochem.

    By the way i see no reason why medical people need know these biochem things!
    Its beside the point of any skill in medicine.
    Diagnosis and prognosis nedd not invoke any memory of biochem as i see it.
    It seems like the modern mirror of the middle ages people learning latin for everything.

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    1. I would like my MD to have as much memory of biochemistry as possible. Especially biochemistry with an understanding of evolution. An understanding of both better enables an MD of understanding how antibiotic resistance is a problem for their patients, how viruses can expand their host range, understanding the toxicity of compounds, etc. etc.

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    2. "By the way i see no reason why medical people need know these biochem things!
      Its beside the point of any skill in medicine."

      Which just goes to show that you have no idea what skills are necessary in Medicine.

      Delete
    3. You'll all have to forgive Robert, he just got back from a session of having the leeches removed and a cupping followed by a blood-letting so his black and yellow bile humours are out of wack and he's not his usual coherent self.

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    4. Actually so many problems are said to be psychologicalthe leeches might work very well even today on many.
      I heard its a myth that was used much.
      Come on people.
      It doesn't matter if a doc understands bacteria resistance.
      He just needs to know if the antibiotic he gave is working or if a better one is needed.
      Anybody can do that .
      BioChem seems unrelated to a working doc.
      It seems a unneeded collection of knowledge.
      Thats why nothing is fixed much relative to our times as a advanced society.

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    5. @Robert Byers,

      The MCAT exam is changing in 2015. Doctors (AAMC) have decided to add a lot more questions on biochemistry because they think it's essential that pre-med students have two semesters of biochemistry and molecular biology.

      This must confuse you.

      Have you ever had a complete physical? Do remember all those blood tests? What did you think they were for? Did you think the test for glucose concentration was just to see if your blood would taste sweet to a vampire?

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    6. "Come on people.
      It doesn't matter if a doc understands bacteria resistance.
      He just needs to know if the antibiotic he gave is working or if a better one is needed. Anybody can do that. BioChem seems unrelated to a working doc."

      *facepalm*

      Jesus, Byers, when one thinks you could not possible embarrass yourself more, you keep surprising everyone.




      Delete
  9. Larry while yes the competencies in biochemistry span what we consider two semesters of material, they are saying it can be done in one semester. It can if you are teaching a memorization course without understanding biochemistry. It would be a very boring course.

    We are getting pressure at my liberal arts college to have such a course. We are refusing. We teach for understanding and our biochemistry courses are designed to be interactive and challenge students to apply knowledge/concepts from previous contexts to understanding chemistry in a particular context, life. Given the context, evolution is essential.

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  10. Dominic Nikel asks,

    I would like to assemble a cell by accident. What should I do? I wanna put everything in the test tube and then assemble by accident the cell in perfect conditions. Please tell me what I should do ....

    First, you need an incubator because everything has to be kept warm.

    Second, you need a pond ... preferably a little one.

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    1. @Larry,

      It doesn't look like you were being serious after all.

      Both Venter-who focuses on "top-down" creation of a cell and Rasmussen-who focuses on "bottom-up" creation of a cell, believe that this process can happen only if ALL ESSENTIAL COMPONENTS are not necessarily in a warm pond, but within some kind of a membrane, as information and energetics need to cooperate to sustain each other’s production. While metabolism-your favorite suspect for the first step of the origins of life-seems important, it however doesn't seem very vital without other essential components and most of all outside of some kind of a membrane.

      Delete
  11. Dominic Nikel:

    I believe professor Moran is having a good laugh at your expense. He doesn't really believe that a cell can self-assemble in a warm pond. It's impossible, even if all the needed components were there and at the same time. Many have already tried to do that and have failed miserably. Professor Moran has to claim that it is possible, because of his status and position, but he is not stupid and knows that it would take more than just the components being in the warm pond to assemble a cell, even if they had billions of years.

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    1. @ Milos

      You are not suggesting Larry is lying to me are you?

      Delete
  12. Maybe someone could comment on how evolution just happened to make the bee orchid?

    The bee orchid had to:

    1)correctly guess the right insect for pollination.

    2)paint(yes look at the plant) the correct size, color and gender of the bee

    3)develop pheromones that draw the male bee in

    All this was done without any feedback mechanism. Tell me how long does it take for a blind artist to draw a bee with the right colors and size without any prior knowledge of a bee.

    ReplyDelete