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Author
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Topic: Are Biological Systems Designed for Discovery?
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John Bracht
Member
Member # 5
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posted 24. December 2002 16:08
The ideas I want to outline here are inspired by some recent work by Jay Richards and Guillermo Gonzalez, who have recently finished writing a book, "The Priveleged Planet," which has not yet been published. However, I've attended several lectures where they presented their ideas, and I want to take some of these ideas and extend them into the realm of biology (Jay and Guillermo focus on cosmology).
The basic argument in the book is that our universe is structured in such a way that the very conditions that allow complex life to exist are the same conditions that maximize our ability to learn about the universe. For example, our moon is precisely the right size and distance from earth to stabilize its tilt, which allows for stable seasons and weather patterns. The moon also happens to be the precise size and distance from earth to generate perfect solar eclipses--which have greatly facilitated our study of the universe. For instance, studies of the sun's corona are done during a perfect eclipse. A vital test of Einstein's theory of relativity was performed during a solar eclipse, looking for a lensing effect of the light of a star as it curved around the sun--and only by blocking most of the sun's light during an eclipse was such lensing observable.
The solar eclipse phenomenon was discussed earlier here on ISCID.
At any rate, after looking at numerous other conditions that seem to be simultaneously required for life's existence and also provide maximum "observability" or "discoverability", Jay and Guillermo come to the conclusion that the universe is "designed for discovery".
If the universe is in some sense designed for discovery, it makes sense that we might find the same phenomenon in other areas besides cosmology. In particular, it would seem reasonable to suspect that biology might also be "designed for discovery"--designed in such a way that biological investigation is facilitated.
I've identified three characteristics of biological organisms that seem to be optimal in terms of allowing biologists to make discoveries: 1. the modular nature of proteins, 2. the chemistry of DNA, and 3. the existence of excellent model systems.
1. Proteins are strings of amino acids divided up into "domains" which usually have distinct functions. These domains are often structurally independent, so they can be swapped and mixed to generate novel proteins. This has many advantages in the laboratory. It is possible to study protein-protein interactions, for example, by attaching different fluorescent domains to two proteins; if they come into proximity (interact in a complex) the two fluorescent domains will alter their emissions in characteristic ways as energy is transmitted from one to the other. More simply, it is possible to add a "tag" to a protein-encoding DNA sequence and transfect that DNA into a tissue culture cell line. These cells will now express the protein with its "tag" (usually a small domain with characteristic shape, that can be recognized by an antibody). The protein can then be "pulled down" from lysed cells using an anti-tag antibody--and any other proteins that are complexed with the protein in question can be pulled down also. This is probably the most common method for detecting protein-protein interactions, and it relies critically upon the modular nature of proteins--if the addition of the "tag" sequence disrupted the structure of the protein under study, it would not interact normally with other proteins in the cell and would not yield any useful information. The modular nature of proteins is useful in another way: scientists can swap out domains to characterize their regulation or functionality. One example of this I recently read had to do with combining the cytoplasmic end of a transmembrane receptor with the extra-cellular domains of another receptor. That way, the chimeric receptor would activate the same downstream molecules as the original receptor, but it would be activated by a different ligand (signalling protein that binds the extra-cellular region). This allows researchers to tease apart subtle differences in function, and also to isolate the effects of one receptor from the effects of others that might be similar (isolating the desired receptor's effects from endogenous receptors that might confound the results).
2. Just last week I was talking with Dr. Scott Emr, a yeast biologist at UCSD who I spent the last six weeks working for. My project involved a lot of PCR (polymerase chain reaction), which is a technique that allows one to quickly make billions of copy of a given sequence of DNA in a test-tube. There are some remarkable tricks that can utilize PCR to "sew" two different pieces of DNA together, or add specific tags or end-sequences that can target the amplified DNA for recombination at a given site. As we were talking about how amazing this process really is, he made the comment that "this all relies on the beauty of DNA chemistry." He pointed out that it's rather remarkable that we can take a test-tube, add the DNA-making enzyme from cells (actually, the enzyme comes from a thermophillic bacteria), add the basic ingredients of DNA, and some "primers" (short pieces of DNA that start the process of duplication) and with cycling temperature, the whole system works to replicate DNA--all outside of a cell. Dr. Emr pointed out that this ability to quickly amplify DNA would be extremely difficult if, for instance, one had to sequentially add 20 different enzymes and multiple different reaction conditions. Yet PCR is one of the foundations of modern molecular biology--nearly every paper in the field will describe experiments that utilize PCR in one form or another. Again, it almost seems as if biological systems are meant be studied in the test-tube.
3. There are some model organisms that just amaze me. I spent the summer working with C. elegans, the nematode. This organism has many excellent features, like short life-cycle (3 days for one generation), clearly identifiable stages in its life-cycle (allowing selection of organisms at the same stage for experiments), and the fact that they are hermaphrodites. This greatly simplifies the task of generating homozygous recessive mutations and also of maintaining stable, recessive lines. Yet "males" (which produce only sperm) can be produced (and do arise at a low frequency spontaneously) to provide the ability to cross lines and do complementation studies and out-crossing (which is used to clean up the genome after isolation of novel mutants). Another amazing feature of C. elegans: it can survive freezing at -80C! This allows various lineages of interest to be stored indefinitely, and a "collection" of different genetic mutants can be easily stored.
Of course, the ease with which yeast can be genetically manipulated is the stuff of legend. The ability to take a piece of DNA, transfect it into yeast cells, and have it integrate into defined locations is an amazing trait that allows the yeast field to be one of the fastest-advancing areas in biological research. While C. elegans is the organism of choice for studying development and differentiation in multicellular organisms, yeast is by far the best choice for studying basic cellular processes that are ubiquitous to all cells.
These two model systems seem to be pretty much ideal. I've spent a fair bit of time wondering what traits would make C. elegans a better model system, and I can't think of any. I don't have as much experience with yeast, but it seems remarkably optimal also.
It curious whether these features of life that seem "investigation-friendly" are built into the laws of the universe, or whether life could have taken on other, "non-investigation-friendly" configurations. Could life exist with non-modular proteins? Could life exist with DNA that is impossible to replicate outside of a cell? Are model systems key parts of the ecosystem, or could they exist in a way that still props up the food-chain without added benefit to biological investigation?
If the answer is "no", if life HAD to be the way it is simply because of the way the universe is configured, then one comes to a front-loading type of question: could the universe have been different, such that biological systems were not investigator-friendly?
If the answer is "yes", then the question occurs: can we consider the "investigator-friendly" forms of biological systems to be an indepently specified pattern? Can we calculate the probability that biological systems fit that pattern? In other words, it may be that this is a novel form of complex, specified information that can be used to drive a design inference. Of course, it is difficult to speculate about how many other possible forms life can take, since we have only one form to look at.
So, is biology "designed for discovery"? Are there features of biology that seem to be sub-optimal for investigation? Is the universe such that evolution will only produce "investigator-friendly" life-forms? Or is there contingency such that there are many possibilities out of which the investigator-friendly ones were selected?
These ideas are very speculative and obviously difficult to get a handle on. I'm not sure we can ever empirically answer many of the questions I've raised in this post but would like to hear other's feedback on the topic.
John
P.S. I want to wish everyone a very Merry Christmas and a wonderful new year!
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Granville Sewell
Member
Member # 550
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posted 03. January 2003 09:05
John,
I like the term, "designed for discovery." I think that all of science was designed for discovery; in particular, my field, mathematics. The layman, who thinks of mathematics as consisting of arithmetic, and "higher mathematics" as long division :-), is always shocked to find that there are hundreds of mathematical journals out there, covering as many subfields of pure and applied mathematics. But not only are those journals there, they are filled every month with fascinating and entertaining (and often useful!) articles, each discovering new ideas in fields so rich that none of them are close to being exhausted.
I can understand how one can look at current events, and history, and in particular the history of religion, and not see God. But how one can look at any field of science and not see God is something I will never understand.
Granville Sewell
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zygotecowboy
Member
Member # 220
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posted 09. January 2003 15:45
I had no intention of mocking John’s post. Mocking implies contempt, and I hold no contempt for John or his postings. I was attempting to create an informative parody, making light of a situation with the intention of illuminating the pitfall of the reasoning. This is a method practiced by numerous philosophers, and indeed, I had Voltaire in mind.
Regardless, since the post was deemed not in line with the spirit of Brainstorms, I’ll remove the offending material as requested. I think the point is made well enough by subsequent posters, including the moderator. Those that are interested, though, may find the original post here.
Of course, John isn't the first IDist to posit this sort of idea.From here.
quote:
Anything showing complex design demonstrates that there is a designer. When you see a house, you know there was a house builder. When you see a painting, you know there was a painter. Even the atheistic evolutionist does understand this because in their quest for finding life beyond earth they using radio-telescopes trying to find some pattern in what they are picking up. They are looking for design in order to prove an intelligent designer.
What would you say if I took a can of soda and told you it was the result of billions of years of evolution. That the magnetic properties of the metal drew the metal atoms together in such a way that they formed a cylinder with a bottom, and then after millions of years a brown, sweet liquid formed inside. After more millions of years a top formed with lid that could open easily. Then after more millions of years it became colored, in this case, with red, gold and white in such a way that it read in English, "Diet Dr. Pepper" and "12 FL OZ." That sounds pretty foolish doesn't it, and even more so if I added that thousands of these soda cans evolved and then arranged themselves in rows of 3 by 2 with a plastic material forming around their tops so six of them can be carried at a time.
But consider what people believe about something like a banana. The outside is a biodegradable wrapper that changes color according to the condition of what is inside. Green is too early, Yellow is just right and Black is too late. It has a "pop top" and seems so that it can be easily opened and still protect the contents from contamination. You can eat this even if your hands are dirty - perfect for boys and men! Its shape is perfect for the human hand and mouth, and if you hold it correctly, it even bends toward you for easy consumption. Nutritionists tell us that the contents of a banana are one of the best foods for humans. It is easily digested and provides the body with energy as well as vitamins and minerals. The banana also contains seeds inside it which can grow into a banana tree and then produce more bananas. Try planting a soda can and see what grows! The banana is infinitely more complex than a can of soda and demonstrates the design of a wise creator, yet many people willingly ignore the obvious to claim it is the product of the chance mixing together of molecules in chemical reactions over millions and millions of years. It is more plausible to get the soda can by evolution than a banana - hence a good name for a banana is "The Atheist Nightmare."
[ 11. January 2003, 13:28: Message edited by: zygotecowboy ]
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Moderator
Administrator
Member # 1
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posted 09. January 2003 16:21
Zygotecowboy,
Your post is inappropriate to Brainstorms. You adopt a tone of mockery and ridicule rather than the careful, thoughtful analysis that is expected of participants here.
You may well have a legitimate point, namely, that the appearance that biological systems are "designed for discovery" is an artifact of our discovery process. However, you method of bringing this point out is completely out of the spirit of Brainstorms.
If you wish your post to remain on this thread, please edit it to make a specific, thoughtful argument about why biological systems are only artifactually "designed for discovery"--otherwise, I'll delete your post in a few days.
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Argon
Member
Member # 276
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posted 09. January 2003 19:07
Mod 1 wrote to 'zygote cowboy':
quote:
Your post is inappropriate to Brainstorms. You adopt a tone of mockery and ridicule rather than the careful, thoughtful analysis that is expected of participants here.
I do not know much of 'zygote cowboy's posting history but personally, I thought his comments went straight to the point in a humorous way -- Which sometimes helps clarify things (Voltaire's Candide comes to mind). Much better than dryly commenting that the moon hasn't always been at just the right distance to produce 'perfect' solar eclipses. Or that the "ease with which S.cerevisiae can be genetically manipulated is the stuff of legend" only because many talented and hard-working people labored for hundreds of person-years to develop the methods that make it "easy" today. I remember when yeast molecular biology was anything but easy and I don't think one would have to look too hard to find a yeast species that is an absolute bear to work with.
YMMV.
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yersinia
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Member # 324
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posted 09. January 2003 21:29
At least as important as the work put into making model organisms "easy to use" is the simple fact that out of X million species we have picked the ones that were easy to experiment on to do experiments on. Mice and Drosophila were not chosen at random...
The other point enhancing the utility of model organisms is the discovery that homology extends much further back than we had a right to expect. Homology allows the inference of common descent and degree of relatedness which allows us to gauge the strength of inferences from one organism to another.
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