Spinning Wheels
by BradfordMike has highlighted the importance of proteins. Proteins are involved in all sorts of cellular functions including their own synthesis. Each step in the pathway to protein synthesis involves proteins. That includes the regulation of genes (whether or not a gene coding protein will be expressed), the transcription process and translation. It takes proteins to generate proteins. The proteins involved in the synthesis of other proteins are synthesized by the same cellular mechanisms they become part of.
There are two ways of analyzing the role of proteins. Proteins illustrate the interdependence of cellular functions and the dependence of cells on the proper coordination of its separate parts. That in turn is evidence of downward causation- a paradigm favorable to ID.
But we could continue to approach the matter of life's origin solely from a reductionist perspective. After all reductionism has led to success in other fields and provides an inductive argument for its continued utilization in origin of life research. Spinning wheels can keep an occupant in the same place but rabbits have another means of advancing.
May 7th, 2008 at 2:54 pm |
Implicit in this is the assumption that biology is currently "spinning its wheels" due to a reductionist approach. This is absolutely false, biology is one of the most rapidly advancing sciences right now. You assert that Biology is somehow broken simply because its not reaching the conclusion you want. In reality Biology is doing just fine with current methods.
Comment by Todd Berkebile — May 7, 2008 @ 2:54 pm
May 7th, 2008 at 3:07 pm |
Todd,
Did you really think that Bradford was saying that "Biology is broken"?
Fascinating.
Comment by chunkdz — May 7, 2008 @ 3:07 pm
May 7th, 2008 at 5:05 pm |
chunkdz:
I hope he wasn't really thinking that. After all I did use the phrase "matter of life's origin" and not "matter of biology." The point being patterns of results and non-results count for something. If nothing else a reappraisement is in order. Noone is suggesting throwing out the baby with the bathwater.
Comment by Bradford — May 7, 2008 @ 5:05 pm
May 7th, 2008 at 8:23 pm |
I guess I didn't realize that "spinning its wheels" was meant as an endorsement of continuing to use the reductionist approach of Biology to move towards understanding OOL. Here I thought that meant this approach was flawed, deficient, broken. So stop playing games and be forthright: Bradford do you think biology as a scientific field of study following the ideologies it uses today is an adequate tool for reaching eventual understanding of the OOL or do you think its somehow broken and unable to ever accomplish that goal? Saying "reductionism has led to success in other fields" is certainly an attempt to imply it has not led to success here. I feel biology is moving us towards eventual understanding of OOL even though it cannot currently present a meaningful hypothesis. No other discipline has presented a meaningful OOL hypothesis either but only biology is moving us closer by increasing understanding of the cell and its components.
Comment by Todd Berkebile — May 7, 2008 @ 8:23 pm
May 7th, 2008 at 9:11 pm |
You need to stop playing games. I made a distinction between OOL and biology as a whole. Reductionist approaches have been miserable failures with regard to OOL.
Comment by Bradford — May 7, 2008 @ 9:11 pm
May 7th, 2008 at 9:26 pm |
Hi Bradford,
But there is a significant caveat that illustrates just how hard is to break away from the ambiguity that is our reality. The ribosome is effectively a ribozyme. If this was not true, your argument could go a very long way.
Then again, the whole RNA world has as a basic assumption and argument that strengthens my case – RNA was replaced by a superior design material – proteins.
Rabbit? Duck? Takes yer pick.
Comment by MikeGene — May 7, 2008 @ 9:26 pm
May 7th, 2008 at 10:17 pm |
A tiny machine which is part of the mechanism of life. Ribosomes occur both as free particles within cells and as particles attached to the membranes of the endoplasmic reticulum. A ribosome is made of about 40% protein and 60 % nucleic acid. It is composed of four nucleic acid molecules and about 70 different proteins.
A ribosome consists of two parts, a larger one and a smaller one, each of which has a characteristic shape. Ribosomes are very numerous in a cell and account for a large proportion of its total nucleic acid.
Comment by Bradford — May 7, 2008 @ 10:17 pm
May 8th, 2008 at 12:06 am |
So then you see the continuing advancements in biology as separate and/or unrelated to eventually making meaningful theories about OOL? I see no clear distinction to be made, the only thing that separates OOL from modern biological research is the exact knowledge gap that the research is working to shrink. In this respect all these advancements are moving us closer to a theory for OOL. Only proteins make proteins, what's the point? This is just a revision of the older argument that only humans make humans but due to advances in biology we now all accept the evidence of common descent. The same argument has simply been pushed further down into the knowledge gap. What's truly different about the argument this time? Why given the success of biological science so far do you assume it will fail this time? Reductionist perspectives have not only succeeded in other fields, they have succeeded and continue to succeed in biology. Is there evidence that biological sciences are approaching some limit beyond which current methods will become ineffective? Or do you simply want the final answer more quickly than the research can be performed? Are you willing to make up an answer simply to reach the answer more quickly? I repeat my question: do you think biology as a scientific field of study following the ideologies it uses today is an adequate tool for reaching eventual understanding of the OOL or do you think its somehow broken and unable to ever accomplish that goal?
Comment by Todd Berkebile — May 8, 2008 @ 12:06 am
May 8th, 2008 at 1:05 am |
What separates OOL from the rest of biology is results. While we make impressive strides in understanding cells and cellular functions we see little but continued speculation about origins. While medical progress advances by leaps and bounds OOL is by comparison sterile. We are mapping genomes while pondering how basic biochemicals would come about in an extra-cellular world. The contrast is striking.
Comment by Bradford — May 8, 2008 @ 1:05 am
May 8th, 2008 at 6:59 am |
Biology is one of the most rapidly advancing sciences right now largely because of molecular biology. And molecular biology was spawned when scientists decided to import engineering concepts into biology.
Comment by MikeGene — May 8, 2008 @ 6:59 am
May 8th, 2008 at 8:06 am |
MikeGene wrote:
I am not exactly sure, Mike, what you mean by importing engineering concepts into biology. Perhaps you should say a bit more about that. If you meant to draw parallels with engineers at, say, Intel, whose goal is to create a new processor, that would be the wrong analogy. But maybe I'm misreading you, so I'll await your further thoughts.
My perspective, shared by my wife (who is a biochemist), is that rapid progress in molecular biology is a typical example of what happens in any branch of science when researchers get a new experimental tool. PCR, for instance, provides a quick way to analyze specific regions of the DNA, enabling researchers to do lots of things from paternity tests to amplification of trace amounts of ancient DNA to genome mapping. It has thus generated a wealth of new information to chew on. Experiments are key to scientific progress.
Comment by olegt — May 8, 2008 @ 8:06 am
May 8th, 2008 at 8:12 am |
Molecular biology? Sounds like straightforward reductionism.
Comment by Zachriel — May 8, 2008 @ 8:12 am
May 8th, 2008 at 8:37 am |
olegt:
I agree and this explains a lack of OOL breakthroughs. New technology is used to study living organisms as olegt points out. As we have studied living organisms over the years we have discovered surprisingly intricate mechanisms and functions whose origin does not yield to a biochemical analysis of such mechanisms. For example, how would one explain the origin of genomes? The approach has been to assume they evolved from RNA based dynamics. This would hopefully explain both the origin of information storage and catalytic functions. But would it?
The chemical origin difficulties inherent to RNA are imposing enough. Ideas as to how it would arise in a prebiotic world are not lacking. None inspire great confidence. But it is their most critical property that is most resistent to explanation for it demands a chemically based explanation of molecular symbolism. Nucleic acids are able to code for biological functions because the order of nucleotides has functional significance. But why would blind chemical reactions induce the nucleotide patterns observed in highly conserved transferases, lyases, ligases, hydrolases and oxidoreductases? Since such enzymes are proteins there is no reason to assume that would even occur in an RNA world. Ah but those ribozymes right? Your initial enzymes. And the initial genome? Where is the specificity enabling replication of systems and passing on of genetic information that can evolve?
The questions posed reference historic events for which there are no organisms to study even in theory. The minimal genomes of obligate parasites are relatively small but well beyond theoretical proto-cell concepts. So how is technology applied? What experiments are relevant to the underlying questions?
Comment by Bradford — May 8, 2008 @ 8:37 am
May 8th, 2008 at 8:43 am |
It is quite amazing what can be discovered when we have cells to study.
Comment by Bradford — May 8, 2008 @ 8:43 am
May 8th, 2008 at 8:53 am |
I really would like to know what you would consider a OOL breakthrough. In the past decades biologists have studied intensively minimal genomes, synthetic life, RNA enzymes, …
I bet we could make an argument that xyz explains the lack of 'cancer biology' breakthroughs.
And, as an aside, the fact that amino acids have an affinity to the codon that encodes them can easily explain the 'most critical property that is most resistent to explanation'.
Comment by hrun — May 8, 2008 @ 8:53 am
May 8th, 2008 at 9:11 am |
Sure we've studied them. Life is characterized by interacting systems of biochemicals whose replication retains function albeit somewhat modified from time to time. Where is experimental evidence showing the emergence of systems?
Explanations are a dime a dozen particularly when you have tRNAs, amino acids and amino acyl enzymes in place. But where's the beef?
Comment by Bradford — May 8, 2008 @ 9:11 am
May 8th, 2008 at 9:30 am |
I think the case can definitely be made that SYSTEMS biology was spawed by importing engineering concepts.
I can't speak for engineering and its relation to molecular, developmental, or organismal biology. You can for get any contribution from engineeringing discipline proper regarding evolutionary biology even though one of the greatest evolutionary biologists, John Maynard Smith, was an engineer….[maybe a couple others if I recall correctly]. Engineers have been notoriously the source of criticisms of evolutionary biology, but they fully participate in systems biology.
1/3 of the engineers at MIT are devoted to systems biology. See Design Revolution at MIT.
Salvador
Comment by Salvador T. Cordova — May 8, 2008 @ 9:30 am
May 8th, 2008 at 9:32 am |
And molecules.
What separates
OOLcancer from the rest of biology is results. Reductionist approaches have been miserable failures with regard toOOLcancer. Therefore we should consider other possibilities (e.g. demons). Why is the assumption thatlifecancer is produced by a series of chemical reactions the default belief? Why would anyone with knowledge of cellular functions be led to this conclusion by that knowledge? Explanations are a dime a dozen.Comment by Zachriel — May 8, 2008 @ 9:32 am
May 8th, 2008 at 9:44 am |
You chose a poor example Zachriel. Much progress has been made with regard to the causes and treatment of cancer. We've learned for example, that failures of regulatory and check-point mechanisms can lead to uncontrolled replication. Chemotherapy now is focused to a great extent on these causes. My wife was diagnosed as having cancer several years ago. She was treated with some of the newest forms of chemotherapy available and her cancer is in remission and prospects look good. Real benefits accruing from relevant research.
Comment by Bradford — May 8, 2008 @ 9:44 am
May 8th, 2008 at 9:45 am |
'Symbolism' is just a type of association. There is no intrinsic barrier to the evolution of such associations.
Once you have replicators, you have evolution. The origin of replicators, and the history of their development is an area of active research. The discovery of autocatalyzing molecules, in vitro evolution of RNA, and the non-random chemical affinity of amino acids for the base triplets that code for them, are important clues to this history.
So you say you have a complete theory of the causes of cancer?
Comment by Zachriel — May 8, 2008 @ 9:45 am
May 8th, 2008 at 9:53 am |
I'm aware that there is no barrier in your mind.
Bradford: But why would blind chemical reactions induce the nucleotide patterns observed in highly conserved transferases, lyases, ligases, hydrolases and oxidoreductases?
Another canard. You need more than SRMs to demonstrate plausible prebiotic cellular pathways.
Bradford: You chose a poor example Zachriel.
We have progress yielding tangible benefits that explain actual events as opposed to the abstract musings typical of OOL.
Comment by Bradford — May 8, 2008 @ 9:53 am
May 8th, 2008 at 10:00 am |
I'll restate for clarity. No intrinsic barrier has been demonstrated.
You had asked a sweeping question. Once, you have replication, you have evolution, and we know that evolutionary processes can build complex structures. A complete history requires far more than the origin of replicators, of course. But that wasn't your question.
In other words, "no".
Comment by Zachriel — May 8, 2008 @ 10:00 am
May 8th, 2008 at 10:10 am |
Zachriel, you seem to think you have a point in your favor by pointing out that we have not conquered cancer and then analogizing this to the state of OOL. It is nowhere comparable. Even a cursory review of many relevant journals reveals documented results related to real cancers. Compare this to research showing not even a complete set of cellular biochemicals arising in extra-cellular environments. The contrast is evident to all but the ideologically blinded.
The point of replication is you don't have it. Life involves replication of systems of many different biochemicals. Decades of research indicates this does not emerge in prebiotic conditions.
Comment by Bradford — May 8, 2008 @ 10:10 am
May 8th, 2008 at 10:18 am |
Cutting out a cancer, or poisoning it, is not a theory of the origin of cancer. Explanations are a dime a dozen.
Comment by Zachriel — May 8, 2008 @ 10:18 am
May 8th, 2008 at 10:31 am |
LOL. Do you know what is meant by poisoning it? One of the exciting developments in the fight against breast cancer is continued refinement of better drugs known as selective estrogen receptor modulators. They come in different varieties and those varieties reflect the cell types which are targeted. Actually the targets are specific cellular mechanisms within cell types. All solid science and markedly different from the speculative exercises that mark OOL.
Comment by Bradford — May 8, 2008 @ 10:31 am
May 8th, 2008 at 10:40 am |
What separates OOL from the rest of biology is about a billion years of time passing. You simply want to jump straight to the end without all that pesky learning in between. We first need to develop the new tools and methods that will allow us to look further back rather than simply peering into the dark and jumping to unfounded conclusions.
Every hypothesis is an assumption, but they aren't simply stating these assumptions like some of their critics do, instead they are continuing to expand our knowledge through specific testable claims and gathering empirical data. This process moves us closer and closer to eventual understanding of the OOL, but it doesn't happen over night. It's taken our big brains and modern forms 100,000 years to get this far of which most of the progress has been in the last few hundred years.
In other words, there's lots of knowledge and hypothesises but none of it is pointing towards the conclusion you want to reach therefore none of it counts as "beef" in your view? This is the fundamental problem, your bias clouds what you consider important and thus your assessment of our progress towards understanding OOL.
His example was intentionally poor, but it seems like a perfect analogy to your position to me. Simply travel back in time a hundred years and people would have been saying exactly what Zachriel said, but now not so many years later the argument seems absurd because breakthroughs have been made. Why will the OOL prove to be different? Why is biology broken such that it can never answer this specific question? You should consider the historical perspective of your argument, you are effectively claiming that the past history of success with similar seemingly impossible challenges will stop when considering the OOL. Yet you cannot answer what is fundamentally different about OOL verse these other major challenges (other than to state we've already made progress in conquering these other challenges).
Comment by Todd Berkebile — May 8, 2008 @ 10:40 am
May 8th, 2008 at 10:49 am |
Yes, as a matter of fact, I do have some idea. But being able to target various tissues is not a complete theory of causation. Sure, there are theories of the causes of cancer, but explanations are a dime a dozen.
I kinda like this handwaving thing. It's actually quite easy and doesn't require a lot of book learnin'.
Comment by Zachriel — May 8, 2008 @ 10:49 am
May 8th, 2008 at 10:50 am |
Todd:
What distinguishes OOL is the absence of all that typifies solid scientific theories.
Comment by Bradford — May 8, 2008 @ 10:50 am
May 8th, 2008 at 10:52 am |
Cancer researchers have something to show for their work. What do you have to show for OOL Zachriel?
Comment by Bradford — May 8, 2008 @ 10:52 am
May 8th, 2008 at 10:55 am |
Bradford: You chose a poor example Zachriel.
Unlike cancer rsearchers you have no reliable object of study. Once in a while a cellular biochemical is discovered outside cells and it is touted as evidence for a process. It is nothing of the kind.
Comment by Bradford — May 8, 2008 @ 10:55 am
May 8th, 2008 at 10:56 am |
You don't think a billion years of time passing should make it any harder to make meaningful statements about the OOL? That seems like an unreasonable expectation.
He has the entirety of biology and all the knowledge gained. You still haven't explained why you think all the knowledge we are gaining is unrelated to eventual understanding of OOL. You simply state that OOL is a separate and unrelated thing therefore none of our advances are moving us towards understanding it.
But then again it seems that so far you have avoided asking every question I've asked of you in this thread. Its hard for me to analyze your position when you won't respond to simple questions concerning it.
Comment by Todd Berkebile — May 8, 2008 @ 10:56 am
May 8th, 2008 at 10:57 am |
I didn't know that science required a utilitarian test.
Cancer researchers are still very primitive in their understanding of cancer. Illustrative of this is that in many cases, doctors still have to resort to the knife, often horribly disfiguring the
victimpatient, often to no avail.As to abiogenesis, in vitro evolution of enzymes is an active area of medical application.
Comment by Zachriel — May 8, 2008 @ 10:57 am
May 8th, 2008 at 10:59 am |
One hundred years ago people studying cancer had large tumors to look at and not much else. Today people studying OOL have millions of living organisms to look at an not much else. I fail to see where this weakens the analogy.
Comment by Todd Berkebile — May 8, 2008 @ 10:59 am
May 8th, 2008 at 11:00 am |
Todd Berkebile: His example was intentionally poor …
Then why not dispense with the waving and verbiage. Instead of arguments simply cite the emergence of replicating biological systems. Not a cell or even basic functions. But something other than yak yak yak.
Comment by Bradford — May 8, 2008 @ 11:00 am
May 8th, 2008 at 11:03 am |
In vitro development of enzymes can have medical benefits. It has nothing to do with abiogenesis but does demonstrate the power of engineering.
Comment by Bradford — May 8, 2008 @ 11:03 am
May 8th, 2008 at 11:05 am |
Gladly. Now, you do the same.
Please provide a valid and complete theory of the cause of cancer. Or simply admit it might be
demonsan unnamed designer using an unspecified mechanism for some undetermined purpose.Comment by Zachriel — May 8, 2008 @ 11:05 am
May 8th, 2008 at 11:05 am |
Todd, science is demonstrative. It does not matter that you think knowledge is OOL related. You don't have to argue these things when you can point to the evidence.
Comment by Bradford — May 8, 2008 @ 11:05 am
May 8th, 2008 at 11:06 am |
Cut the crap Zach. Your demon nonsense is getting tiresome.
Comment by Bradford — May 8, 2008 @ 11:06 am
May 8th, 2008 at 11:33 am |
For example, in Bartel's Lab, they will generate a few quadrillion random RNA sequences, then select from among those that have the desired activity, replicate them, then repeat the process. This demonstrates the plausibility of a spontaneous origin of replicators, the significance of evolutionary processes, as well as providing new medical benefits.
In other words, you can't provide a valid and complete theory of the cause of cancer. This returns us to hrun's comment.
And, as we have seen, he was correct.
Comment by Zachriel — May 8, 2008 @ 11:33 am
May 8th, 2008 at 11:52 am |
It demonstrates the wonders of intelligently guided processes.
Bradford: Your demon nonsense is getting tiresome.
No. He was wrong. There have been breakthroughs. Another example of the difference between real research and OOL.
Comment by Bradford — May 8, 2008 @ 11:52 am
May 8th, 2008 at 12:06 pm |
In other words, "no".
In other words, "no".
Billions of dollars have been spent on the problem. What makes you think that the failed materialistic methods of the past will one day find such a theory?
Comment by Zachriel — May 8, 2008 @ 12:06 pm
May 8th, 2008 at 12:15 pm |
Zachriel, don't bother posting edited responses that misinform readers. Your previous comment noted this:
My comment: (There have been breakthroughs.) was made in reply to hrun's erroneous belief that:
The ommision of which is quote mining. If your intent is to derail the theme of the thread find something else to do.
Comment by Bradford — May 8, 2008 @ 12:15 pm
May 8th, 2008 at 12:18 pm |
That, and that random RNA sequences can exhibit *functional* enzymatic activity, including the catalysis of the type of polymerization reaction for RNA replication.
I apologize for any misattribution (though I don't think it misrepresented your view). But you forgot to answer the question. Billions of dollars have been spent on finding a complete theory of the causes of cancer. What makes you think that the failed materialistic methods of the past will one day lead to such a theory?
Comment by Zachriel — May 8, 2008 @ 12:18 pm
May 8th, 2008 at 12:27 pm |
From the link;
As I've asked many times previously what is the selection criteria for an extended RNA primer and what rational basis is there for thinking the end result of this process (if it were sustainable) is a cell?
Comment by Bradford — May 8, 2008 @ 12:27 pm
May 8th, 2008 at 12:29 pm |
Medical research, including cancer research, is a success. My wife and millions like her in the world are examples of it.
Comment by Bradford — May 8, 2008 @ 12:29 pm
May 8th, 2008 at 12:35 pm |
People were cured of cancer even in ancient times, by use of the knife. In more modern times, by interferring with the ability of the cancer to survive and spread. This technical ability has little to do with understanding the origins of cancer. But let me help you out. Much of the research is tied in with the evolutionary theory, both common descent, and cells within the organism. But I agree that science will continue to be an effective means of probing the question.
Comment by Zachriel — May 8, 2008 @ 12:35 pm
May 8th, 2008 at 12:42 pm |
Current research is focused largely on what causes disruptions of cell cycle mechanisms. This is off topic.
Comment by Bradford — May 8, 2008 @ 12:42 pm
May 8th, 2008 at 12:49 pm |
As the events in question happened billions of years ago, the evidence is quite scant, but many advances have been made. For instance, the non-random chemical affinity of amino acids for the base triplets that code for them is consistent with abiogenesis, and unexplained by design. And the fact that random RNA sequences can have *functional* activity is also consistent with abiogenesis. In addition, modern phylogenetics adds strong support to a common evolutionary origin for microbiological structures.
Comment by Zachriel — May 8, 2008 @ 12:49 pm
May 8th, 2008 at 12:58 pm |
This has nothing to do with OOL. If you wish to believe that amino acids, tRNAs, enzymes facilitating the linkage between amino acids and tRNA, and a replicating genome come about through unspecified means, that is your right. It takes a great deal of faith and you might secure the appropriate religious tax classifications from the IRS for an organization promoting this. Don't pretend you are promoting a plausible scientific theory though.
Comment by Bradford — May 8, 2008 @ 12:58 pm
May 8th, 2008 at 1:07 pm |
Zachriel:
Bradford:
Nothing? Riiiiiight. It might just explain the genetic code, that's all. Nothing to see here, folks.
Really, Bradford, your dishonest posturing and moving of goal posts doesn't go unnoticed.
Comment by Raevmo — May 8, 2008 @ 1:07 pm
May 8th, 2008 at 1:18 pm |
Thanks for the specificity. A preponderence of amino acids in some tRNAs might explain the genetic code. Keep the faith.
Dishonesty? For not keeping your faith? Find something else to do.
Comment by Bradford — May 8, 2008 @ 1:18 pm
May 8th, 2008 at 2:15 pm |
Why would assumed chemical affinity be consistent with a process that yields systems of interacting biochemicals, whose function became part of the synthesis of proteins, when the anticipated approach- a gradual generation of the synthesis process through piecemeal additions- corresponds to no specified selection criteria. The theme of the post is that related analyses are plausible within a holistic framework. Yet gradual construction through a blind watchmaker cannot have the functional systems of interacting proteins as an outlook. That requires foresight, which contrary to the quoted comment, is explained by design.
Comment by Bradford — May 8, 2008 @ 2:15 pm
May 8th, 2008 at 7:45 pm |
If I read you correctly, that's the crux. In contemporary organisms the anticodon doesn't directly contact the amino acid. If primoridal proteins were originally templated by the nucleotide sequence, then we might see a chemical affinity between the bases and the amino acids. Later, when more complex mechanisms evolved, this assignment would be a non-random vestige of their origin. A fossil.
Knight, R.D. and Landweber, L.F. (2000). Guilt by association, Journal RNA
Comment by Zachriel — May 8, 2008 @ 7:45 pm
May 8th, 2008 at 8:37 pm |
No time to talk tonight. Maybe tomorrow.
Comment by MikeGene — May 8, 2008 @ 8:37 pm
May 8th, 2008 at 8:38 pm |
Zachriel, when the term primordial proteins is used there is a need for a theoretical context. Everyone understands what is meant by random mutations, transcription function, metabolism, selection and many more concepts because they apply to well understood cellular contexts. In a non-cellular world primordial proteins need a context which makes their cause comprehensible. Proteins are intrinsically interactive. That's the stuff of cellular functions. If there is no equivalent in a precellular world vagueness and imprecision become big conceptual barriers.
Comment by Bradford — May 8, 2008 @ 8:38 pm
May 9th, 2008 at 7:29 am |
Hmmm. Here's a question. What is the difference between molecular biology and biochemistry?
Comment by MikeGene — May 9, 2008 @ 7:29 am
May 9th, 2008 at 8:21 am |
Very difficult to tease apart. But in general they are considered to be somewhat overlapping.
From Wikipedia: Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis and learning how these interactions are regulated.
Common usage in Biology labs sometimes reduces Molecular Biology basically to certain lab techniques- primarily the manipulation of DNA for experimental purposes.
Comment by hrun — May 9, 2008 @ 8:21 am
May 9th, 2008 at 8:23 am |
molecular biology, a branch of biology dealing with the ultimate physicochemical organization of living matter and especially with the molecular basis of inheritance and protein synthesis.
biochemistry, chemistry that deals with the chemical compounds and processes occurring in organisms.
There's quite a bit of overlap. The former is a branch of biology, the latter a branch of chemistry. They meet in the middle, as it were. Microbiology is clearly reductionist.
Wikipedia: With the hope of understanding life at its most fundamental level, numerous physicists and chemists also took an interest in what would become molecular biology. In its modern sense, molecular biology attempts to explain the phenomena of life starting from the macromolecular properties that generate them.
Comment by Zachriel — May 9, 2008 @ 8:23 am
May 9th, 2008 at 6:10 pm |
Hi Zachriel,
Those are fuzzy, vague definitions that really don’t explain why we have two disciplines.
Look at it this way guys. How would a mainstream, non-controversial molecular biologist describe the process of protein synthesis? Well, something like this:
To make a protein, a molecular machine, known as the ribosome, translates a messenger RNA molecule using the genetic code.
Machine. Message. Translate. Code.
Hmmm. Doesn’t sound very "biochemical" to me. Where do we normally find such concepts?
Comment by MikeGene — May 9, 2008 @ 6:10 pm
May 9th, 2008 at 6:34 pm |
Hi olegt,
It’s pretty clear that scientific giants such as Crick, Jacob, Monod, and many other pioneers in molecular biology, borrowed heavily from information theory, cybernetics, and even electronics. In fact, some considered it a fad. Molecular biology is a field of science that focuses mostly on nucleic acids, proteins, and their interaction. The discovery of DNA as a sequence of subunits led scientists to think of a code and information theory entered in the realm of biology. And while this was going on, the black box of gene regulation was opened (the lac operon) and concepts from cybernetics/electronics took prominence in the realm of biology. We are still feeling the reverberations of these remarkable discoveries along with the conceptual imports, even to the point where today a leading evolutionary biologist researches and explains evolution as something that uses switches and “packets of information.”
There is no doubt that experiments are key to scientific progress, but experiments involve at least two essential elements. First, they require instruments/tools. In molecular biology, electron microscopes, centrifuges, electrophoresis apparatus, and even radioisotopes, opened an unseen world. Second, the data must be interpreted and appreciated. Here, the engineering concepts helped open that unseen world. (BTW, as an aside, all of this helps us appreciate why science does not discover Truth; science is a function of its tools and perspective).
As far as PCR goes, the main tool there is, you guessed it, a protein called Taq polymerase. In fact, nowadays, the two new tools opening doors are our own advanced computers/programming and the nano-devices we isolate and exploit from life itself.
Comment by MikeGene — May 9, 2008 @ 6:34 pm
May 9th, 2008 at 6:38 pm |
Not so fast. We know that protein-dependent evolutionary processes can build complex structures.
Comment by MikeGene — May 9, 2008 @ 6:38 pm
May 9th, 2008 at 6:39 pm |
Of course the definitions don't explain why we have two disciplines.
Biochemistry has been around for hundreds of years and dealt mainly with the chemical analysis of biomolecules. The term Molecular Biology was coined less than a hundred years ago… and even then was already somewhat vague– but it did focus primarily on two macromolecules and their connection (DNA and proteins).
Molecular Biology really took of later when restriction enzymes, ligases and further down the road sequencing and PCR became mainstream tools to manipulate DNA for experimental purposes.
I'm curious, you seem to think that there is some importance to the fact that Molecular Biology and Biochemistry are two disciplines. Why is that?
Or how about this: Do you think there is no overlap between Biochemistry, Molecular Biology, Genetics, Molecular Genetics, Cancer Biology, Systems Biology, Signal Transduction, Bioinformatics, Biophysics, …
What would be the significance of the overlap or the lack of complete and clear demarcation between these disciplines?
Comment by hrun — May 9, 2008 @ 6:39 pm
May 9th, 2008 at 7:02 pm |
I’m curious, you cut away the follow-up point in the posting you replied to. Why is that?
Did I say anything about importance? Nope. Pay attention – I didn’t not have time to post last night and I surely did not have time to post anything long this morning. So I asked a question that I naively thought might provoke some thinking. My apologies for not remembering that I am dealing with people who are in constant BattleMode.
Comment by MikeGene — May 9, 2008 @ 7:02 pm
May 10th, 2008 at 3:25 am |
[BattleMode]My, my. Touchy today.
I meant no offense. Just like you asked a question, I asked one. I was actually somewhat baffled by your follow-up post, after you actually got an answer to your question about Biochemistry and Molecular Biology. Especially since it was so easy to look up the various definitions of Molecular Biology and Biochemistry on the web, I assumed you were trying to make a specific point.
You might have noticed that in both of my posts I actually tried to answer your questions: Namely WHAT Biochemistry and Molecular Biology are and WHY we have two disciplines. But apparently neither of these answer actually seemed to get to the point that you were trying to make.
And the reason why I cut away the follow-up point in the posting was because I didn't get it. I would guess that the answer to my question (namely why YOU think this distinction is important) might actually shed some light on what you meant by the part that I left out.[/BattleMode]
Comment by hrun — May 10, 2008 @ 3:25 am
May 10th, 2008 at 9:07 am |
That's correct. We know that evolutionary processes *can* build complex structures. As you point out, we have at least one actual example—as well as mathematical models and simulations. This answers Bradford's objection concerning "a chemically based explanation of molecular symbolism." Evolution is a plausible mechanism.
Comment by Zachriel — May 10, 2008 @ 9:07 am
May 10th, 2008 at 9:27 am |
That would be a modern interpretation and doesn't explain the origins of a separate field of study. However, molecular biologists have generally been interested in the physical structure of molecules. Then again, biologists often study macroscopic structures in terms of their physical characteristics and machine analogues.
That was your original statement which concerned the historical origins of molecular biology. Certainly, chemistry, biology and physics were important. Your reference to "engineering concepts" seems rather vague—but maybe it makes some sense if you consider Wu's 1929 hypothesis of protein folding to be an "engineering concept". Molecular biology is reductionist, in any case.
Comment by Zachriel — May 10, 2008 @ 9:27 am
May 10th, 2008 at 10:31 am |
Zachriel:
We don't have a single example of a chemically generated genetic code and zero evidence that evolution takes place in the absence of such a code. So let's look at a reference you supplied:
And where did all those amino acids come from in this imaginary world. This is the first thing about which a reader must beware when looking at defenses of abiogenesis. The existence of critical biochemicals is introduced without a causal chain delineating why Nature would favor that condition. This is why such accounts are correctly labeled just so stories. In cells biochemicals known as tRNAs are critical elements needed to correctly sequence amino acids in a polypeptide chain. Right at the outset we have a problem. We can define what a required amino acid in a protein would be when the protein is identified. It enables protein function or at the very least does not compromise it. But protein function is conveniently omitted from the analysis. Why? Because it would gum up natural selection arguments to have to discuss protein function. When you do that you invoke the need for other biochemicals like DNA which stores the information about amino acid sequencing. Strike two. Insufficient clarity. More:
That's rather convenient. We have a code in place lacking three amino acids. Strike one resurfaces. Aminoacyl tRNA synthetases are protein enzymes essential to enabling the translation of the genetic code. Interestingly these enzymes contain the three alluded to missing amino acids which only show up later. Strike three and one out. Not only are biochemicals introduced without causal genesis, we have to reinvent the nature of them to satisfy a chemical evolution paradigm. Aminoacyl tRNA synthetases observed to contain twenty amino acids must have originally only contained 17. Where is Occam's razor when you need to shave speculation spawned by a paradigm need?
Comment by Bradford — May 10, 2008 @ 10:31 am
May 10th, 2008 at 11:54 am |
Oddly enough, this appears to be a legitimate question when talking about abiogenesis, but asking "Where did the designer and all his tools come from in this imaginary world?" is considered by many a completely illegitimate critique of ID.
Comment by hrun — May 10, 2008 @ 11:54 am
May 10th, 2008 at 12:29 pm |
That wasn't what I had claimed (but you are assuming your conclusion). I suppose you can continue to raise any number of objections to positions I haven't taken.
But first, let me make sure I understand your position. Do you claim that there is a demonstrable and intrinsic barrier to (spontaneous) abiogenesis?
In vitro RNA evolution.
Comment by Zachriel — May 10, 2008 @ 12:29 pm
May 10th, 2008 at 12:57 pm |
hrun:
That's why it is important to distinguish exactly what is inferred. I'm not going to infer a designer to which personal attributes are ascribed. There are some issues that are beyond the scope of empirical inquiry. That would also apply to explanations based on "natural laws." There is ultimately no way to trace a causal trail beyond the birth of the universe(s). Because at that point you need to explain issues that are inherently speculative and lie in the realm of metaphysics.
Comment by Bradford — May 10, 2008 @ 12:57 pm
May 10th, 2008 at 1:03 pm |
I'm claiming the absence of a plausible theoretical framework within which abiogenesis can be assessed. That is not the same as asserting a barrier but practically speaking amounts to a claim that abiogenesis is not an empircally supported idea; a claim that can be supported with referenced data.
Comment by Bradford — May 10, 2008 @ 1:03 pm
May 10th, 2008 at 1:04 pm |
Huh? No personal attributes? Are you being serious? For one, supposedly the designer is intelligent. That's not an attribute? Then the designer is always assumed to have certain capabilities (depending on what you believe he actually designed), like being able to create a universe, being able to create life, …
So what designer do you think you can infer without any 'personal attributes' that has any related to, let's say, the OOL problem?"
You know, to me it appears that on the one hand you arbitrarily pick any assumed or hypothesis precondition to try and discredit a theory about abiogenesis. And in my eyes that is perfectly legitimate. But, you can't then at the same time turn around and not recognize that the same holds true for any theory that includes an intelligent designer. If it's a legitimate question where the amino acids came from, it's a legitimate question on where the designer came from.
Comment by hrun — May 10, 2008 @ 1:04 pm
May 10th, 2008 at 1:13 pm |
hrun, I've been in too many of these exchanges to not know what comes next. Of course intelligence is an inferred attribute. But then comes a slew of questions that are unanswerable based on physical evidence. That unanswerable questions are beyond the scope of reductionism is as legitamate a philosophical position as the atttribution of our current state of affairs to gaps.
Comment by Bradford — May 10, 2008 @ 1:13 pm
May 10th, 2008 at 1:14 pm |
So the you agree that you arbitrarily exclude the question 'Where did xyz come from?' as far as ID is concerned, but you think it is a perfectly legitimate question for any other OOL theory?
I'm glad we don't have to go down a road of long winded discussion. I just wanted to make sure that this double standard is out in the open.
Comment by hrun — May 10, 2008 @ 1:14 pm
May 10th, 2008 at 1:28 pm |
hrun:
You're misaliging the analogies. It is perfectly legitimate to ask where an intelligent inference comes from and why it is a necessary component of theory as opposed to a superfluous element as per LaPlace. An IDist then is obligated to note nucleic acids (or whatever is included with the claim) and their physical properties as part of an explanation. He also must allow for a non-teleological falsification. I don't inquire where the universe and its laws ultimately come from and ask for an explanation because that goes to a why question- the proper analogy to questions about the exact nature of a designer.
Comment by Bradford — May 10, 2008 @ 1:28 pm
May 10th, 2008 at 1:36 pm |
Misaligning analogies?
Is it not true that you can question any of the given preconditions for the hypothesized OOL theories? Like where did the proteins come from? Where did the amino acids come from? How did the DNA code come about? I bet if I were to invest some time on this board I could find countless questions posed by you about the various OOL scenarios.
Can you in any way give me a cogent explanation of why it is not legitimate to question ID with the same type of question: Where did the designer come from? Where did his tools come from? Where did his raw materials come from?
Can anybody else chime in? Is there really a legitimate reason one such questions are fair game for all OOL theories except for one?
Comment by hrun — May 10, 2008 @ 1:36 pm
May 10th, 2008 at 2:20 pm |
Nobody knows. It's a brick wall that reason cannot scale.
Questions asked, questions answered.
Any naturalistic line of inquiry must likewise end the same way.
Comment by kornbelt888 — May 10, 2008 @ 2:20 pm
May 10th, 2008 at 2:27 pm |
Please elaborate.
Comment by kornbelt888 — May 10, 2008 @ 2:27 pm
May 10th, 2008 at 2:33 pm |
Mike Gene says:
No worries, Mike. We all forget once in a while. Remember: This thread is titled Spinning Wheels. Spin is the key word here.
Comment by nobody — May 10, 2008 @ 2:33 pm
May 10th, 2008 at 2:46 pm |
kornbelt888,
I believe this is what Zach is referring to.
Comment by nullasalus — May 10, 2008 @ 2:46 pm
May 10th, 2008 at 2:49 pm |
Kornbelt, I'm sorry, but you didn't really answer my question. At least not in a way that I can actually understand what your opinion is: Is there a reason why such questions are fair game for all OOL theories (materialistic ones) except for one (ID)?
Comment by hrun — May 10, 2008 @ 2:49 pm
May 10th, 2008 at 2:59 pm |
Any question is a fair question. However with an ID conjecture, at the point where the agent designs, we are no longer dealing with merely a-telic natural laws, that we have direct access to outselves- we are dealing with agents with intelligence, foresight and intent. That would seem to complicate matters a great deal with regards to the kinds of questions we could ask about how they designed and implemented their productions.
By the way, an ID conjecture need not be non-materialistic. Humans design things all the time, and I assume you consider us to be purely materialistic.
Comment by kornbelt888 — May 10, 2008 @ 2:59 pm
May 10th, 2008 at 3:24 pm |
I understand that the actions of the agent are not a-telic. But how does that relate to the point of where the designer and his materials come from? I'm not asking HOW the designer designed.
I was asking Bradford a question analogous to his: He wanted to know where the amino acids in Zach's scenario came from. I wanted to know where the designer, his tools and his materials came from.
Bradford seems to think that his question is a fair line of inquiry, while mine is not. I would like to find out why.
Good. All the more the reason to treat the ID conjecture the same way as one would treat the non-ID conjecture. If it's fair game to ask where the amino acids came from, it's fair game to ask where the designer, tools and materials came from, isn't it?
Comment by hrun — May 10, 2008 @ 3:24 pm
May 10th, 2008 at 3:37 pm |
Like I said, any question is a fair question. But isn't "I don't know" a fair answer? At any rate, how does that keep us from pursuing the issue of proximate cause of earth life? Informative answers to your questions sure would help, but are they necessary to answer the proximate cause of earth life? Maybe, maybe not. That's still an open question.
You bet. But do you think investigating ID conjectures is an unworthy endeavor unless we can definitively answer your questions about the designer and his tools?
Comment by kornbelt888 — May 10, 2008 @ 3:37 pm
May 10th, 2008 at 3:43 pm |
hrun,
It's fair to ask in the sense that all questions are fair to ask. But taken as a criticism - 'if we can't explain the designer's origins, then we can't use design to explain an event' - is another issue.
If we found an artifact that strongly appeared to be a sculpture or an engineering device - but it was 20myo - you couldn't shoot down the design contention by demanding the designer be explained, and that it couldn't have been a human. There would exist many theoretical possibilities for a designer, but trying to argue 'no design, because we have no information on the designer' wouldn't get you very far.
On the flipside, theories that involve a designer could still be questioned if they asserted the use of amino acids by the designer. "Where did the amino acids come from?" We're still following a trail of material evidence in that case, but even the presence of a designer doesn't mean the assumption of amino acids is valid even though you could imagine a designer using such. Along the lines of how saying the Mona Lisa was designed doesn't on its own lend validity to the claim of 'Photoshop was used'.
Comment by nullasalus — May 10, 2008 @ 3:43 pm
May 10th, 2008 at 3:44 pm |
Sure it is a fair answer. I wonder if Bradford would agree with that as well, though. He seems to try and dismiss the scenario that Zach was talking about by calling into question where the amino acids came from.
Bradford:
Seems like Bradford wants to discount a specific OOL scenario, just because of a lack of 'a causal chain delineating why Nature would favor that condition.' By this reasoning, I think we can safely dismiss any theory that contains a designer, design tools and design material as 'just so stories' until we have 'a causal chain delineating why Nature would favor the existence of a designer, design tools and design materials'. Would you agree?
Oh no. I think it is a futile endeavor, but that's a completely different story.
Comment by hrun — May 10, 2008 @ 3:44 pm
May 10th, 2008 at 3:48 pm |
Nullasalus, this is not the objection I'm making. I'm calling on Bradford to fairly apply his standards to all OOL theories. As I wrote in the previous post, Bradford wants 'a causal chain delineating why Nature would favor that condition' otherwise a theory is only 'a just-so story'.
Likewise, Bradford should call for 'a causal chain delineating why Nature would favor the existence of a designer, his tools and materials' or else he should also label OOL scenarios based on a designer only 'a just-so story'.
Comment by hrun — May 10, 2008 @ 3:48 pm
May 10th, 2008 at 4:01 pm |
hrun,
Considering perspective of a Designer are often such where Nature itself is seen as a tool for the agent, I don't think that reasoning works out.
But even assuming a designer that's within nature, back to the artifact example. The same arguments could conceivably go on; we'd have no evidence of a designer, aside from one artifact that was the design itself. When it came to amino acids, I read Bradford as arguing that it's possible the situations described came to pass - and that they could easily fit into the design view as well.
Bradford's not rejecting any data here. He's asking for evidence of claims, even while taking the position that said claim can fit in a design view. Just because an event could have been designed doesn't mean that all claims of method have the same grounding.
Comment by nullasalus — May 10, 2008 @ 4:01 pm
May 10th, 2008 at 4:04 pm |
Moving past reductionism.
ScienceDaily (May 9, 2008)
http://www.sciencedaily.com/re...
Comment by nobody — May 10, 2008 @ 4:04 pm
May 10th, 2008 at 4:19 pm |
So then you DO think it is legitimate that such questions are applied to all OOL scenarios except for one.
That's not what Bradford wrote. He wrote, referring to a scenario put forth that assumed the presence of amino acids that without 'a causal chain delineating why Nature would favor that condition' the scenario remains a just-so story. He didn't write anything about such a scenario also fitting with a design theory.
The point remains, apparently asking for 'a causal chain delineating why Nature would favor [a certain] condition' is a legitimate objection to all OOL scenarios but the ID scenarios. I really don't see what would warrant this double standard, but so be it.
The only reason WHY I think this would be legitimate is if one were to claim that ID theories are metaphysical by nature, while the other OOL scenarios are scientific by nature. But I don't think that's where Bradford wants to go with this.
If both fall into the 'scientific' category, then both types should be submitted to the same kind of questions. And if failure to answer such questions labels one theory a just-so story, it should likewise label all theories without such answers just-so stories.
Never said Bradford was rejecting data. I said that Bradford was applying a double standard: One for ID theories and on for all other OOL theories.
Comment by hrun — May 10, 2008 @ 4:19 pm
May 10th, 2008 at 4:23 pm |
Could you explain to us why their experiments are not reductionist by nature? As far as I understand reductionism, it means 'an approach to understanding the nature of complex things by reducing them to the interactions of their parts'.
Isn't that exactly what they are doing in their experiments? Trying to understand the nature of the cell cycle by studying the expression of the 6000 genes in the yeast genome?
Comment by hrun — May 10, 2008 @ 4:23 pm
May 10th, 2008 at 4:29 pm |
Though no one has proposed a complete theory of abiogenesis, there is nothing preventing the proposal of limited hypotheses which can be assessed. For instance, there is evidence that genetic transcription evolved from more primitive precursors.
Comment by Zachriel — May 10, 2008 @ 4:29 pm
May 10th, 2008 at 4:34 pm |
hrun,
Why would assumed chemical affinity be consistent with a process that yields systems of interacting biochemicals, whose function became part of the synthesis of proteins, when the anticipated approach- a gradual generation of the synthesis process through piecemeal additions- corresponds to no specified selection criteria. The theme of the post is that related analyses are plausible within a holistic framework. Yet gradual construction through a blind watchmaker cannot have the functional systems of interacting proteins as an outlook. That requires foresight, which contrary to the quoted comment, is explained by design.
Bradford can correct me, but I took that to mean that it wasn't as if he was ruling out given scenarios because they were 'competition to design', but that design could flow with said data - and nevertheless there were questions to address regarding it.
Some things in the universe may be ultimately unknowable, but we can still draw the lines between what data we have and what data we don't. Nothing wrong with that, eh?
I suppose one response would be that a dynamic relationship between a large number of genes producing a situation that could not be fully understood by knowledge of the smallest constituent 'parts' of the organism alone is not reductionistic. An emergent relationship resulting from, but not fully reducible to, those parts.
Comment by nullasalus — May 10, 2008 @ 4:34 pm
May 10th, 2008 at 4:47 pm |
So how do you interpret the following statement by Bradford after Zach wrot