In short, biologists are aware of the limitations of their assumptions and have some solid idea as to when their assumptions are valid or not.
Doing the bioinformatics will help a researcher sort through the dramatically large number of gene sequences to find a set which is likely enriched for the characteristic they are looking for. They know they will miss interesting cases which don't match the models used. Without these sorts of predictions, they would have to rely on random guessing as a strategy with a much lower payout.
We have a pretty good idea on this one. Specific polymerases have specific sequences which they respond to, defining the start sequences of genes. It is possible we have missed some polymerase, but the likelihood is low given the extensive searches which have been done for them. As well, regions which are genes have a distinctively different character than regions which are not genes (at least in the general sense).
2. We can predict the protein sequence from the sequence of the gene.
We also have a pretty good idea about this, due to decades and decades of biologists trying to figure out the answer to this problem. The genetic code turns out to differ in some organisms from what we think of as the default. Sometimes multiple amino acids are coded for by the same sequence of bases, and so multiple proteins are produced from the identical coding region of DNA. Sometimes proteins are produced with modified amino acids, which are not explicitly coded for in the DNA of the gene, but rather by the activity of other proteins defined elsewhere by DNA. (This is a stochastic process and interference in the distribution of outcomes can sometimes result in pathological consequences.) In some organisms, the DNA is decompressed into RNA which is then translated into protein in a more typical way. (Extra bases are incorporated into the RNA in a repeatable way that results in amino acids added which were not defined in the sequence of DNA of the gene being added to proteins.) There's a whole bunch of stuff on alternate splicing, which we explicitly know that we don't know how to predict, that produces variations in protein sequence from a single gene sequence.
3. One protein can not be the product of two genes.
There are plenty of ways in which two separate genes can produce an identical protein. This actually happens ALL THE TIME in mammals, since we have two copies of every gene and most of these pairs have identical sequence. Even if the genes produce the identical protein through different mechanisms, if the protein is identical... then the protein is identical.
4. We have a good understanding of what the functions of the proteins in the training set are.
We do have a good idea of what the functions of the proteins in the training set are. See all of molecular biology for your citations.
5. If two proteins have similar sequence, they must have similar functions.
This is explicitly known to be false and is not expected under the evolutionary model. Look up the category of proteins known as 'crystalins' for a specific case counter to your assumption.
6. One protein has one function.
It is generally thought that there is a primary function for every protein. All things in biology are fuzzy, such that every protein probably has secondary side reactions or functions which may or may not be biologically relevant. (Arsenic is poisonous to us because our enzymes have a hard time distinguishing it from Phosphorous, so the enzymes which incorporate phosphorous also 'function' to incorporate arsenic.)
7. A protein has a function.
Any protein synthesized by a cell costs energy. Under the evolutionary model of biology, proteins which don't have a function should have been discarded because their synthesis was wasting energy. That said, lots and lots of proteins are continuously created and then rapidly degraded because they were improperly folded or had other problems which brought them to the attention of intracellular systems with the 'function' of degrading such errant protein and returning their components to the cell for more productive use. Some genetic diseases are the consequence of the buildup of proteins which are otherwise non-symptomatic, but don't get degraded properly by the degradation systems.
Outrage is not what I experience, annoyance at having wasted the time to read about someone claiming something they didn't actually do... that will probably always annoy me.
In this case, there are 3D printing systems which don't rely on gravity the way he claims... but this guy's company doesn't have them. http://www.youtube.com/watch?v=SYbw1oSzPVA is one example.
I really get annoyed when people describe something they've thought of (or something they've found) as something they've invented. Nice idea Covey, let me know when it exists.
...or some downstream developmental gene....or......or......or...
The doctors studying the girl should already have a very good idea of what has gone wrong. The article gives the impression they have no clue... which could either be an issue with science journalism or with doctors playing biologist.
The syndrome description as given is remarkably like Cretinism. Cretinism typically results from insufficient iodine levels in the diet during early childhood. This person may have mutation(s) which mimic the damage caused in Cretinism.
I can define a time on that remote star easily. A black hole eating the star or flinging it at near relativistic speeds doesn't really cause a problem with the existence of time progressing, only of the rate of progression of time. I cannot tell how much time has passed for that star, only that it has.
There have actually been instances of people being sickened because the potatoes some farmer bred to be more pest-resistant turned out to have exceedingly high levels of solanine (the normal potato insecticide and why you should not eat green potatoes). To keep this from happening again, all large-scale potato breeders routinely test their creations for enhanced solanine content.
If produce was labeled as GMO, without further details, you still don't have any information to make an educated guess as to what the probabilities are of a problem. GMO-labelling needs to include what genes were added from what organism, as well as what they do in the resulting organism, to be of any informative use.
As well, the bacteria that you think of are rather distinctly newcomers on the biology scene and differ in much of their basic machinery from the bacteria we derived from. If you want to study the bacterial types that we derived from, you need to examine what are now referred to as the Archaea. This indicates there were major evolutionary shifts within bacteria since the time we went our own direction as Eukaryotes (estimated to be from 2.0 to 3.5 Bya), which is a negative mark to your central thesis of "not much of significance has happened to bacteria since 3.5 Bya".
And since they're not just going after Google, they will be even faster to change their policy once they start sending out the license fee requests and actually get peoples' attention.
I would wager that the fine-tuning to current conditions is all that the evolution of life is and as such is the only part that tells anything about it.
The idea that living things of that time would have already had the basics of our molecular machinery is a hypothesis. We have no way to know if living things from that era used the same systems that we now do, rather than something simpler and less efficient. The majority of them could have used entirely different molecular systems, only to later be dramatically out-competed by a relative latecomer that we derive from.
Even now there are variations in the basic molecular machinery used by different organisms. Some organisms have genomes that are de-compressed (as in information compression, not physical compaction) before being translated into proteins, most don't. Many organisms don't use the same DNA coding scheme that you use. Many organisms use alternate DNA bases, totaling to more than four base-pair combinations that are biologically important. Many don't use histones, while others do. Some have cytoskeletons composed of actin and tubulin fibers, some don't.
----
Under some reasonable models of abiogenesis, the central metabolic circuits intrinsic to all living things developed before living things had DNA or cell membranes. Cells could easily have formed and been actively 'alive' without having any sort of central genetic molecule (they would have been less efficient at replicating themselves). As such, it is perfectly possible that the fossils being discussed came from cells which explicitly did not share much of our core molecular systems.
We can learn things from early biology that we do not expect, but we won't learn things from early biology if we simply assume that we know what was going on. (This is a general statement that applies to all of scientific endeavor.)
It is really a mistake to think of the evolution of bacteria having ended at any point. They've been evolving just fine since they formed, as evidenced in part by your existence (not a joke, as you/we are derived from those early life forms). There is reasonable reason to believe that what we think of as bacteria (Eubacteria specifically) evolved after we (Eukaryotes) went our own way. At the time quoted, the atmosphere of our planet was significantly different than now, so the basic physiology of the 'bacteria' of the time would have been rather different than most 'bacteria' now.
I had a friend in college who came from central Africa... to our school in central Texas. He really could not handle the heat that I took in stride. He expressed exactly the same misunderstanding that your family had, but the opposite polarity.
There are not good reasons to think the northern areas were as diverse as the Amazon up until the 15th century and there are VERY good reasons to expect the more northern forests to be depleted relative to the Amazon.
The amazon has tree types which were common before the Chicxulub impactor, which resulted in a splashing of material up and over most of North America. Much of living things on North America were wiped out at this time. For much of the continent in the times after the impact, the largest land vertebrates were turtles who rode out the devastation under water/ground. Fungus was one of the most common life forms after the impact, as all the trees/etc died and rotted.
The periodic cycles of glaciation experienced by the northern hemisphere continents have a dramatic impact on tree species diversity. When the ice comes south, no trees survive under it. When the ice moves north, the more weedy tree species which can rapidly spread north come to represent more of the population. Every cycle depletes the population of tree (and other) species in the region.
The environment of the Amazon has been MUCH more stable over the long-term, allowing species counts to increase to the maximum allowable by evolutionarily found niches, without the periodic reductions seen in North America. If the impactor had landed slightly differently than it did, we would see a reduced diversity in the Amazon compared to what we have, but the diversity would still be higher than in North America with its periodic glaciations.
Should we instead pay attention to the likes of you, who literally chose to not understand those they're denigrating?
A lack of empathy defines sociopathy, not Aspergers. You seem to be confusing the two.
Aspergers do tend to pull away from the things they find difficult/painful/traumatic, just like anyone else. Unfortunately for them, many of the every day emotional and physical experiences of your life are the sort of things they find difficult/painful/traumatic. You are right in a limited sense, that they can't imagine how to mimic you as you go about your day blithely doing what they find so painful.
Interestingly, that you don't see this at all places you far closer to the sociopathic personality type than the Aspergers you denigrate so easily.
Or should we instead pay attention to the likes of you, who have literally chosen to not understand those they are denigrating?
You are describing Aspergers as if it were sociopathy. Sociopaths do not feel empathy for others, this is the explicit definition of sociopathy.
Aspergers individuals instead feel what you consider everyday emotional and physical sensations as being sufficiently painful or traumatic that they choose to avoid them. You are correct in a sense, as an Aspergers individual will not understand how they can mimic you as you blithely go through your life doing what is incredibly difficult/painful for them to do.
Interestingly, as you didn't even notice this, you are much closer to a sociopathic personality compared to what an Aspergers is.
The immunity that babies get from the mother's blood is in the form of antibodies. After birth, the antibodies are no longer being replenished and break down. By the time the antibodies have basically disappeared, the baby's immune system is making its own. Antibodies are transferred through breast-feeding, at a lower efficiency, so there is a continuum.
In the case of bottle-babies, they would have to be protected form exposure until they can get vaccinations... although at this point we can already manufacture antibodies which could be given therapeutically as a replacement for the blood/milk transferred antibodies.
Tin atoms in solder under voltage migrate to sharp points, leading to the growth of very thin whiskers. These whiskers eventually can bridge components leading to shorts, and they also introduce noise to the electrical system as they change its reception characteristics.
The technical solution to this problem is to add more lead to the solder or to use higher temperature solders which don't include tin. Higher temperature solders are more expensive to work with, while lead has (more or less rightfully) become a boogeyman metal of late, so the problem of tin-whiskers has been increasing in recent years.
Slashdot Mirror
In short, biologists are aware of the limitations of their assumptions and have some solid idea as to when their assumptions are valid or not.
Doing the bioinformatics will help a researcher sort through the dramatically large number of gene sequences to find a set which is likely enriched for the characteristic they are looking for. They know they will miss interesting cases which don't match the models used. Without these sorts of predictions, they would have to rely on random guessing as a strategy with a much lower payout.
1. We have accurate mapping of the genes.
We have a pretty good idea on this one. Specific polymerases have specific sequences which they respond to, defining the start sequences of genes. It is possible we have missed some polymerase, but the likelihood is low given the extensive searches which have been done for them. As well, regions which are genes have a distinctively different character than regions which are not genes (at least in the general sense).
2. We can predict the protein sequence from the sequence of the gene.
We also have a pretty good idea about this, due to decades and decades of biologists trying to figure out the answer to this problem. The genetic code turns out to differ in some organisms from what we think of as the default. Sometimes multiple amino acids are coded for by the same sequence of bases, and so multiple proteins are produced from the identical coding region of DNA. Sometimes proteins are produced with modified amino acids, which are not explicitly coded for in the DNA of the gene, but rather by the activity of other proteins defined elsewhere by DNA. (This is a stochastic process and interference in the distribution of outcomes can sometimes result in pathological consequences.) In some organisms, the DNA is decompressed into RNA which is then translated into protein in a more typical way. (Extra bases are incorporated into the RNA in a repeatable way that results in amino acids added which were not defined in the sequence of DNA of the gene being added to proteins.) There's a whole bunch of stuff on alternate splicing, which we explicitly know that we don't know how to predict, that produces variations in protein sequence from a single gene sequence.
3. One protein can not be the product of two genes.
There are plenty of ways in which two separate genes can produce an identical protein. This actually happens ALL THE TIME in mammals, since we have two copies of every gene and most of these pairs have identical sequence. Even if the genes produce the identical protein through different mechanisms, if the protein is identical... then the protein is identical.
4. We have a good understanding of what the functions of the proteins in the training set are.
We do have a good idea of what the functions of the proteins in the training set are. See all of molecular biology for your citations.
5. If two proteins have similar sequence, they must have similar functions.
This is explicitly known to be false and is not expected under the evolutionary model. Look up the category of proteins known as 'crystalins' for a specific case counter to your assumption.
6. One protein has one function.
It is generally thought that there is a primary function for every protein. All things in biology are fuzzy, such that every protein probably has secondary side reactions or functions which may or may not be biologically relevant. (Arsenic is poisonous to us because our enzymes have a hard time distinguishing it from Phosphorous, so the enzymes which incorporate phosphorous also 'function' to incorporate arsenic.)
7. A protein has a function.
Any protein synthesized by a cell costs energy. Under the evolutionary model of biology, proteins which don't have a function should have been discarded because their synthesis was wasting energy. That said, lots and lots of proteins are continuously created and then rapidly degraded because they were improperly folded or had other problems which brought them to the attention of intracellular systems with the 'function' of degrading such errant protein and returning their components to the cell for more productive use. Some genetic diseases are the consequence of the buildup of proteins which are otherwise non-symptomatic, but don't get degraded properly by the degradation systems.
Outrage is not what I experience, annoyance at having wasted the time to read about someone claiming something they didn't actually do... that will probably always annoy me.
In this case, there are 3D printing systems which don't rely on gravity the way he claims... but this guy's company doesn't have them. http://www.youtube.com/watch?v=SYbw1oSzPVA is one example.
I really get annoyed when people describe something they've thought of (or something they've found) as something they've invented. Nice idea Covey, let me know when it exists.
...or some downstream developmental gene. ...or... ...or... ...or...
The doctors studying the girl should already have a very good idea of what has gone wrong. The article gives the impression they have no clue... which could either be an issue with science journalism or with doctors playing biologist.
The syndrome description as given is remarkably like Cretinism. Cretinism typically results from insufficient iodine levels in the diet during early childhood. This person may have mutation(s) which mimic the damage caused in Cretinism.
I can define a time on that remote star easily. A black hole eating the star or flinging it at near relativistic speeds doesn't really cause a problem with the existence of time progressing, only of the rate of progression of time. I cannot tell how much time has passed for that star, only that it has.
No time has passed for the light since it left the star. Time has passed for the star since the light left it.
There have actually been instances of people being sickened because the potatoes some farmer bred to be more pest-resistant turned out to have exceedingly high levels of solanine (the normal potato insecticide and why you should not eat green potatoes). To keep this from happening again, all large-scale potato breeders routinely test their creations for enhanced solanine content.
If produce was labeled as GMO, without further details, you still don't have any information to make an educated guess as to what the probabilities are of a problem. GMO-labelling needs to include what genes were added from what organism, as well as what they do in the resulting organism, to be of any informative use.
You're correct in that it is not 'evolution by natural selection'. You're incorrect in that it is still 'evolution'.
Mutation creates anew, selection winnows, evolution is the sum of both effects.
The selection can be 'natural selection' or 'directed selection' and the result is still change over time, otherwise known as evolution.
He knew that he was right.
As well, the bacteria that you think of are rather distinctly newcomers on the biology scene and differ in much of their basic machinery from the bacteria we derived from. If you want to study the bacterial types that we derived from, you need to examine what are now referred to as the Archaea. This indicates there were major evolutionary shifts within bacteria since the time we went our own direction as Eukaryotes (estimated to be from 2.0 to 3.5 Bya), which is a negative mark to your central thesis of "not much of significance has happened to bacteria since 3.5 Bya".
And since they're not just going after Google, they will be even faster to change their policy once they start sending out the license fee requests and actually get peoples' attention.
I would wager that the fine-tuning to current conditions is all that the evolution of life is and as such is the only part that tells anything about it.
The idea that living things of that time would have already had the basics of our molecular machinery is a hypothesis. We have no way to know if living things from that era used the same systems that we now do, rather than something simpler and less efficient. The majority of them could have used entirely different molecular systems, only to later be dramatically out-competed by a relative latecomer that we derive from.
Even now there are variations in the basic molecular machinery used by different organisms. Some organisms have genomes that are de-compressed (as in information compression, not physical compaction) before being translated into proteins, most don't. Many organisms don't use the same DNA coding scheme that you use. Many organisms use alternate DNA bases, totaling to more than four base-pair combinations that are biologically important. Many don't use histones, while others do. Some have cytoskeletons composed of actin and tubulin fibers, some don't.
----
Under some reasonable models of abiogenesis, the central metabolic circuits intrinsic to all living things developed before living things had DNA or cell membranes. Cells could easily have formed and been actively 'alive' without having any sort of central genetic molecule (they would have been less efficient at replicating themselves). As such, it is perfectly possible that the fossils being discussed came from cells which explicitly did not share much of our core molecular systems.
We can learn things from early biology that we do not expect, but we won't learn things from early biology if we simply assume that we know what was going on. (This is a general statement that applies to all of scientific endeavor.)
It is really a mistake to think of the evolution of bacteria having ended at any point. They've been evolving just fine since they formed, as evidenced in part by your existence (not a joke, as you/we are derived from those early life forms). There is reasonable reason to believe that what we think of as bacteria (Eubacteria specifically) evolved after we (Eukaryotes) went our own way. At the time quoted, the atmosphere of our planet was significantly different than now, so the basic physiology of the 'bacteria' of the time would have been rather different than most 'bacteria' now.
I had a friend in college who came from central Africa... to our school in central Texas. He really could not handle the heat that I took in stride. He expressed exactly the same misunderstanding that your family had, but the opposite polarity.
There are not good reasons to think the northern areas were as diverse as the Amazon up until the 15th century and there are VERY good reasons to expect the more northern forests to be depleted relative to the Amazon.
The amazon has tree types which were common before the Chicxulub impactor, which resulted in a splashing of material up and over most of North America. Much of living things on North America were wiped out at this time. For much of the continent in the times after the impact, the largest land vertebrates were turtles who rode out the devastation under water/ground. Fungus was one of the most common life forms after the impact, as all the trees/etc died and rotted.
The periodic cycles of glaciation experienced by the northern hemisphere continents have a dramatic impact on tree species diversity. When the ice comes south, no trees survive under it. When the ice moves north, the more weedy tree species which can rapidly spread north come to represent more of the population. Every cycle depletes the population of tree (and other) species in the region.
The environment of the Amazon has been MUCH more stable over the long-term, allowing species counts to increase to the maximum allowable by evolutionarily found niches, without the periodic reductions seen in North America. If the impactor had landed slightly differently than it did, we would see a reduced diversity in the Amazon compared to what we have, but the diversity would still be higher than in North America with its periodic glaciations.
Should we instead pay attention to the likes of you, who literally chose to not understand those they're denigrating?
A lack of empathy defines sociopathy, not Aspergers. You seem to be confusing the two.
Aspergers do tend to pull away from the things they find difficult/painful/traumatic, just like anyone else. Unfortunately for them, many of the every day emotional and physical experiences of your life are the sort of things they find difficult/painful/traumatic. You are right in a limited sense, that they can't imagine how to mimic you as you go about your day blithely doing what they find so painful.
Interestingly, that you don't see this at all places you far closer to the sociopathic personality type than the Aspergers you denigrate so easily.
Or should we instead pay attention to the likes of you, who have literally chosen to not understand those they are denigrating?
You are describing Aspergers as if it were sociopathy. Sociopaths do not feel empathy for others, this is the explicit definition of sociopathy.
Aspergers individuals instead feel what you consider everyday emotional and physical sensations as being sufficiently painful or traumatic that they choose to avoid them. You are correct in a sense, as an Aspergers individual will not understand how they can mimic you as you blithely go through your life doing what is incredibly difficult/painful for them to do.
Interestingly, as you didn't even notice this, you are much closer to a sociopathic personality compared to what an Aspergers is.
Or should we pay attention to you, a person who literally has chosen not to understand the people you are denigrating?
Gold star. ;-)
The immunity that babies get from the mother's blood is in the form of antibodies. After birth, the antibodies are no longer being replenished and break down. By the time the antibodies have basically disappeared, the baby's immune system is making its own. Antibodies are transferred through breast-feeding, at a lower efficiency, so there is a continuum.
In the case of bottle-babies, they would have to be protected form exposure until they can get vaccinations... although at this point we can already manufacture antibodies which could be given therapeutically as a replacement for the blood/milk transferred antibodies.
I like how he made the handle transparent.
Nobody seems to have yet mentioned tin-whiskers.
Tin atoms in solder under voltage migrate to sharp points, leading to the growth of very thin whiskers. These whiskers eventually can bridge components leading to shorts, and they also introduce noise to the electrical system as they change its reception characteristics.
The technical solution to this problem is to add more lead to the solder or to use higher temperature solders which don't include tin. Higher temperature solders are more expensive to work with, while lead has (more or less rightfully) become a boogeyman metal of late, so the problem of tin-whiskers has been increasing in recent years.